Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F13 I1 R1 57 60.3 2567246 98.7% 2533871 146.1

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGCTCGGTGGTCGGGCACAGCACTACGCATTGGCAGTGGTAACGCTCGAGCTGCTGATGATAATGGCCCAGTTGCTCGGGCGACAGGTTACCCAGGTTGGCACCGAGCACCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCACCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGCGCGCCAGTTCGTGGCCATCGACAATGGCGGCACGGCGGCCCAGCAATGGCTGCGGTGGCAGCGCTTCG  >  NC_002947_CJ‑RC/1842941‑1843240
                                                                                                                                                      |                                                                                                                                                     
TGCTCGGTGGTCGGGCACAGCACTACGCATTGGCAGTGGTAACGCTCGAGCTGCTGATGATAATGGCCCAGTTGCTCGGGCGACAGGTTACCCAGGTTGGCACCGAGCACCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCC                                                                                                                                                       >  NB501016:282:H2V7GAFX2:4:11607:9085:10177/1‑151 (MQ=60)
                 attaactacgcttgggctttgttaaggctggagctgctttttaaaatggcccttttggtcgggctaatGGTTACCCTGGTTGGCACCGAGCACCGCGAACTCGACGGGCCGGCCGGCCGGGCTGGCGGCCTGCACCCCCTGCAGCAACTGG                                                                                                                                      <  NB501016:282:H2V7GAFX2:1:21307:9510:9303/83‑1 (MQ=60)
                  AGCACTACGCATTGGCAGTGGTAACGCTCGAGCTGCTGATGATAATGGCCCAGTTGCTCGGGCGACAGGTTACCCAGGTTGGCACCGAGCACCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCACCCCCTGCAGCAACTGGT                                                                                                                                     <  NB501016:282:H2V7GAFX2:1:21104:20244:11043/151‑1 (MQ=60)
                      CTACGCATTGGCAGTGGTAACGCTCGAGCTGCTGATGATAATGGCCCAGTTGCTCGGGCGACAGGTTACCCAGGTTGGCACCGAGCACCGCGAACTCGAAGGGCCGGCCCGCCAGGCTGGCGGCCGGCCCCCCCCGCAGCAACTGGGCGT                                                                                                                                  >  NB501016:282:H2V7GAFX2:2:11106:14863:16656/1‑150 (MQ=60)
                                       TAACGCTCGAGCTGCTGATGATAATGGCCCAGTTGCTCGGGCGACAGGTTACCCAGGTTGGCACCGAGCACCGCGAACTCGAAGGGCACGCCGGCCTGGCTGGCGGCCTGCCCCCCCAGCAGCAACTGGTCGTAGGAGGCGAACAGGCTC                                                                                                                 >  NB501016:282:H2V7GAFX2:3:11505:16407:18355/1‑150 (MQ=60)
                                                       GATGATAATGGCCCAGTTGCTCGGGCGACAGGTTACCCTGGTTGGCACCGAGCACCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCACCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAG                                                                                                  <  NB501016:282:H2V7GAFX2:3:21403:7770:14978/149‑1 (MQ=60)
                                                                  CCCAGTAGCTCGGGCGACAGGTTACCCAGGTTGGCACCGAGCACCGCGAACTCGACGGGCAGGCCCGCCTGGCTGGCGGCCTGCCCCCCCTGCAGCAACTGGTGCTAGGAGGCGAACAGGCTGACGCAGACGCCGCAGTCATCCAGCTGCT                                                                                     >  NB501016:282:H2V7GAFX2:3:21601:14659:4886/1‑151 (MQ=60)
                                                                            GGGGCGACAGGTTACCCAGGTTGGCACCGAGCACCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCACCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGC                                                                           <  NB501016:282:H2V7GAFX2:3:21411:21835:9991/151‑1 (MQ=60)
                                                                                 GACAGGTTACCCAGGTTGGCACCGAGCACCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCACCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGC                                                                      <  NB501016:282:H2V7GAFX2:4:11406:8348:18843/151‑1 (MQ=60)
                                                                                     GGTTACCCAGGTTGGCACCGAGCACCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCCCCCCCAGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGGTCCAGTGCCTGGCGCGC                                                                  >  NB501016:282:H2V7GAFX2:3:11408:15019:6347/1‑151 (MQ=60)
                                                                                         ACCCAGGTTGGCACCGAGCACCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCACCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGCGCGCCAG                                                               <  NB501016:282:H2V7GAFX2:1:21103:18465:13304/150‑1 (MQ=60)
                                                                                                            ACCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCCCCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGCGCGCCAGTTCGTGGCCATCGACAATGG                                           >  NB501016:282:H2V7GAFX2:3:11603:15197:7557/1‑151 (MQ=60)
                                                                                                             CCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCCCCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCAGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGCGCGCCAGTTAGTGGCCATCGACAATGGC                                          >  NB501016:282:H2V7GAFX2:2:21111:9995:13772/1‑151 (MQ=60)
                                                                                                                     TCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCCCCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGG                                                                                      >  NB501016:282:H2V7GAFX2:1:11106:22147:2414/1‑99 (MQ=60)
                                                                                                                               GGCCGGCCTGGCTGGCGGCCTGCCCCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGCGCGCCAGTTCGTGGCCATCGACAATGGCGGCACGGCGGCCCAGCA                         >  NB501016:282:H2V7GAFX2:3:21403:12310:11144/1‑150 (MQ=60)
                                                                                                                                 CCGGCCTGGCTGGCGGCCTGCCCCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGCGCGCCAGTTCGTGGCCATCGACAATGGCG                                         >  NB501016:282:H2V7GAFX2:1:21106:4575:7188/1‑132 (MQ=60)
                                                                                                                                  CGGCCTGGCTGGCGGCCTGCACCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGCGCGCCAGTTCGTGGCCATCGACAATGGCGGCACGGCGGCCCAGCAATGG                     <  NB501016:282:H2V7GAFX2:4:11512:25252:19494/151‑1 (MQ=60)
                                                                                                                                                     CCCCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGCGCGCCAGTTCGTGGCCATCGACAATGGCGGCACGGCGGCCCAGCAATGGCTGCGGTGGCAGCGCTTCG  >  NB501016:282:H2V7GAFX2:3:21412:4134:5541/1‑151 (MQ=60)
                                                                                                                                                     CACCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGTCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGCGCGCCAGTTCGTGGCCATCGACAATGGCGGCACGGCGGCCCAGCAATGGCTGCGGTGGCAGCGCTTCG  <  NB501016:282:H2V7GAFX2:3:11403:20985:17447/151‑1 (MQ=60)
                                                                                                                                                      |                                                                                                                                                     
TGCTCGGTGGTCGGGCACAGCACTACGCATTGGCAGTGGTAACGCTCGAGCTGCTGATGATAATGGCCCAGTTGCTCGGGCGACAGGTTACCCAGGTTGGCACCGAGCACCGCGAACTCGAAGGGCAGGCCGGCCTGGCTGGCGGCCTGCACCCCCTGCAGCAACTGGTCGTAGGAGGCGAACAGGCTCACGCTGAGGCCGCAGTCTTCCAGCTGGTGCTCCAGTGCCTGGCGCGCCAGTTCGTGGCCATCGACAATGGCGGCACGGCGGCCCAGCAATGGCTGCGGTGGCAGCGCTTCG  >  NC_002947_CJ‑RC/1842941‑1843240

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑