annotate test-data/bfast_out1.sam @ 3:bf1c3f9f8282

Fix for FastqToSam MAX_Q usage detection.
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 03 May 2013 17:13:01 -0400
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1 @HD VN:0.1.2 SO:unsorted GO:none
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2 @SQ SN:phiX174 LN:5386
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3 @PG ID:bfast VN:0.6.4d
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4 random_phiX_region_0 0 phiX174 553 255 50M * 0 0 TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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5 random_phiX_region_1 0 phiX174 3693 255 50M * 0 0 GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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6 random_phiX_region_2 0 phiX174 375 255 50M * 0 0 AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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7 random_phiX_region_3 0 phiX174 3168 255 50M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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8 random_phiX_region_4 0 phiX174 5254 255 50M * 0 0 ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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9 random_phiX_region_5 0 phiX174 5066 255 50M * 0 0 AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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10 random_phiX_region_6 0 phiX174 1226 255 50M * 0 0 CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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11 random_phiX_region_7 0 phiX174 1096 255 50M * 0 0 AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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12 random_phiX_region_8 0 phiX174 535 255 50M * 0 0 CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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13 random_phiX_region_9 0 phiX174 3669 255 50M * 0 0 CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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14 random_phiX_region_10 0 phiX174 4887 255 50M * 0 0 TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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15 random_phiX_region_11 0 phiX174 1849 255 50M * 0 0 TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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16 random_phiX_region_12 0 phiX174 4145 255 50M * 0 0 AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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17 random_phiX_region_13 0 phiX174 1853 255 50M * 0 0 TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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18 random_phiX_region_14 0 phiX174 2800 255 50M * 0 0 CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2300 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:11T38 XA:i:0
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19 random_phiX_region_15 0 phiX174 1910 255 50M * 0 0 AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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20 random_phiX_region_16 0 phiX174 3366 255 50M * 0 0 GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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21 random_phiX_region_17 0 phiX174 2165 255 50M * 0 0 CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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22 random_phiX_region_18 0 phiX174 2051 255 50M * 0 0 TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
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23 random_phiX_region_19 0 phiX174 5099 255 50M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0