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
A1 F58 I1 R1 57 79.2 3360594 98.6% 3313545 146.6

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCCGCGCGTCAG  >  NC_002947_CJ‑RC/5462241‑5462525
                                                                                                                                      |                                                                                                                                                      
GAGCTGCAGCTTAAAGCAGACGAGCGCGCCCAAGCCTAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGAAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTG                                                                                                                                         <  NB501016:282:H2V7GAFX2:2:21306:8572:19020/150‑1 (MQ=60)
       AGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGCGGGCGCCCCcccgggtgccccc                                                                                                                                 >  NB501016:282:H2V7GAFX2:4:11411:6510:11079/1‑138 (MQ=60)
            aacccacacccgggcccccagcccgatgctggcgcgcgggtggcggccggcccccaccatgccgtcccgccacatcaagcccaactgcatgtaccggccaacaaccccgGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAAC                                                                                                                            <  NB501016:282:H2V7GAFX2:3:11512:11155:16806/42‑1 (MQ=60)
              AGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCCCCGGCGCCCCcccgggtccccaagcaaaa                                                                                                                           >  NB501016:282:H2V7GAFX2:4:21607:3628:1840/1‑131 (MQ=60)
                 AGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGGGGCCGCGGGCGCCCCccccggggccccgggaacgagcc                                                                                                                       >  NB501016:282:H2V7GAFX2:2:21112:16786:7886/1‑128 (MQ=60)
                        CGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGGGGCCGCGGGCGCCCCcccgggtgcccccgacacacgccccccccc                                                                                                                >  NB501016:282:H2V7GAFX2:3:21411:22796:4759/1‑121 (MQ=60)
                                     AAGCTGCGGCGTGGGTGGCTGCCCGCCGACAGAAAGCCTACACGCCTCAGAAATCGCCACTGTAATTACCGGCCAACTAAGCCGGCGTGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCA                                                                                                   <  NB501016:282:H2V7GAFX2:3:21401:12658:15130/151‑1 (MQ=60)
                                             gcgggggcggccccccccccccacaacgccccccccccccccaaacccccacggcaccacccgcccaaaaaccCCCGCGGGGGGCCCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAG                                                                                           <  NB501016:282:H2V7GAFX2:1:11308:17449:17575/78‑1 (MQ=60)
                                              ggctggtggatccccgcctcctgcatgccgtgacccttcaccaatccccattgctagtatgggtaatcttcccccgggtGGGGCGCCATGGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGG                                                                                          <  NB501016:282:H2V7GAFX2:3:21405:10542:5228/72‑1 (MQ=60)
                                                      gcgcCCCGCCGCCAGCAAGCCTAGACGCCTCAGCAAGCGCCACTGGACCTACCGGGCAACTACGCCCGCTTGGGGCGCCCGCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGG                                                                                  <  NB501016:282:H2V7GAFX2:3:21505:13849:14938/147‑1 (MQ=60)
                                                          CCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGGGCCCGCGGGGGCCCCGCCgggtgcccaagaaaaacgccccccccccacacaacaagccccagccacgcgccccgggccc                                                                              >  NB501016:282:H2V7GAFX2:4:21407:12424:6835/1‑90 (MQ=60)
                                                                 CCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGGGCCCACGGGCGCCCCcgcgggagccccaggaaagcgcccccccccccccccaaaaacccccccccggccccccggcccccgggggg                                                                       >  NB501016:282:H2V7GAFX2:2:11201:22527:16439/1‑80 (MQ=60)
                                                                    ccacgccgagccgccaccgcaagCGCCACTGGAAGCACCGGCCACATACGCCCGCGCGGGGCGCCCGCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTG                                                                    <  NB501016:282:H2V7GAFX2:3:21508:26414:20065/128‑1 (MQ=60)
                                                                                 CCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGGCCGCGGGCGCCCCcccaggtgccccaggaaaaaaccccccccccacacaaaaaacacccgcaaagcccccgcgcccccctggacggggtgaggtgcgccc                                                       >  NB501016:282:H2V7GAFX2:1:11108:24249:12669/1‑64 (MQ=60)
                                                                                   acacaaacccccactgcaagacccggccaactaccCCCGCGGGGGGCGCCCGCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGAC                                                     <  NB501016:282:H2V7GAFX2:1:11304:25290:12265/116‑1 (MQ=60)
                                                                                     AGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGGCCCCGGGCGCCCCccccgggggccccgaaaaaacccccccccccccccaaaaaacccccaccaagccccccccccccccgcccgggggggagggggggggcgcc                                                   >  NB501016:282:H2V7GAFX2:1:11305:5292:6668/1‑60 (MQ=60)
                                                                                           cgccactgcaagccccggccaccaccGCCCGCGGGGGGCGCCCGGGGGCCCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCT                                             <  NB501016:282:H2V7GAFX2:2:11206:20238:8393/125‑1 (MQ=60)
                                                                                            GCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGGGCCCACCGGCGCCCCcccaggtcccccagaaaaaacccccccccccacaccaacaacaccagccaagccccccgcgacccggggccctgggctctgggggcgcccccccgccg                                            >  NB501016:282:H2V7GAFX2:4:11411:1882:14727/1‑53 (MQ=52)
                                                                                                                                    CCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGA                                    <  NB501016:282:H2V7GAFX2:3:21407:13841:1906/119‑1 (MQ=60)
                                                                                                                                      GCGGGCGCCCCGCCTGTTCCCCTTTAAACTCGCCCCCGCCCACATCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCCGCGCGTCAG  <  NB501016:282:H2V7GAFX2:4:11612:3973:3195/151‑1 (MQ=60)
                                                                                                                                      |                                                                                                                                                      
GAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCCGCGCGTCAG  >  NC_002947_CJ‑RC/5462241‑5462525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑