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
A3 F14 I0 R1 206 76.7 3255580 98.8% 3216513 146.3

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGT‑‑GA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCAC  >  NC_002947_CJ‑RC/1070115‑1070398
                                                                                                                                       |                                                                                                                                                            
GCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑‑TCGA‑‑‑‑GCGCCGCGCGG                                                                                                                                         <  NB501016:282:H2V7GAFX2:1:11202:22488:14292/151‑1 (MQ=60)
      CGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGG                                                                                                                                     <  NB501016:282:H2V7GAFX2:2:21302:20302:16013/149‑1 (MQ=60)
       GGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGC                                                                                                                                  <  NB501016:282:H2V7GAFX2:2:21109:17828:16360/151‑1 (MQ=60)
              CTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGCTTTCATCGCCTGTGAGA‑‑TCGA‑‑‑‑GCGCCGCCCGCGCGGCGCTCGATCT                                                                                                                           >  NB501016:282:H2V7GAFX2:4:11611:11787:4733/1‑151 (MQ=60)
                           GGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTC                                                                                                                                <  NB501016:282:H2V7GAFX2:2:21105:19350:6120/133‑1 (MQ=60)
                             ATCGCTGTGCTGTGAGTGGCTTCCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑‑GCGA‑‑‑‑GCGCCGCGCGGGCGGCGCGCGATCTCACAGGCGATGAAAG                                                                                                            <  NB501016:282:H2V7GAFX2:3:11606:13528:7962/151‑1 (MQ=60)
                                   gggcgGTGGGTGGCTTTCACGCTGAACAAGGCGCGCCCGGCCAAGGGCTGATCGGGTTTGTTCGTACGGGGTATGCCGTTAGGTTTGCGGCGCCTGTGAGA‑‑GCGA‑‑‑‑GCGCCGCGCGGGCGGCGCGCGATCTCACAGGCGATGAAAGCCTAAA                                                                                                      <  NB501016:282:H2V7GAFX2:1:21107:12388:18687/146‑1 (MQ=60)
                                            GTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGT‑‑GAgatcgcgcgccccgcggggggggcgcgctgtgacagggggttaaagccaaaaggccatcgg                                                                                                 >  NB501016:282:H2V7GAFX2:3:21503:11942:3159/1‑90 (MQ=60)
                                                               cgccgcgcccGGCCACGGGCTGATCGGGTTTGTCCCTACGGGGTAGCCCGTTAGGTTTTCGGCGCCTGT‑‑G‑‑‑‑CGACCCCCCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTT                                                                          <  NB501016:282:H2V7GAFX2:3:21506:2756:19301/141‑1 (MQ=60)
                                                               CGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTGCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTT                                                                          <  NB501016:282:H2V7GAFX2:1:21101:21429:17454/151‑1 (MQ=60)
                                                                  CTCGCCTGGCCAAGGGGTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTTGGTTTTCGGCGCCTGTGAGA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACG                                                                              <  NB501016:282:H2V7GAFX2:3:11505:3152:12160/144‑1 (MQ=60)
                                                                                 gcggatggggttttgTCGTAAGGGGTAGGCCGTTAGGTTTTCGGCGCCGGTCAGA‑‑CCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCA                                                        <  NB501016:282:H2V7GAFX2:1:21207:5742:16551/136‑1 (MQ=60)
                                                                                    GATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAAT                                                      <  NB501016:282:H2V7GAFX2:3:21610:7483:17805/150‑1 (MQ=60)
                                                                                              gtgggtatgggttatgcggtttggttttgggcgcctggggGA‑‑TCGC‑‑‑‑GCGCGGCGCGGGCGGGGCTCGATCTCAAAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGTCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCG                                            <  NB501016:282:H2V7GAFX2:1:21102:8365:15724/110‑1 (MQ=60)
                                                                                              GTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGCGA‑‑TCGC‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGC                                           <  NB501016:282:H2V7GAFX2:3:11511:19863:3867/151‑1 (MQ=60)
                                                                                              GTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCG                                            <  NB501016:282:H2V7GAFX2:4:21506:20872:19040/150‑1 (MQ=60)
                                                                                                   TAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAG                                       <  NB501016:282:H2V7GAFX2:1:21201:18957:10773/150‑1 (MQ=60)
                                                                                                    AAGGGGTATGCGGTTAGGTTTTCGGCGCCTGTGAGA‑‑GCGC‑‑‑‑GCGCCGCGGGGGCGGCGCTCGATCTAACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGC                                      <  NB501016:282:H2V7GAFX2:3:21408:12016:14510/150‑1 (MQ=60)
                                                                                                      GGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑‑TCGC‑‑‑‑GCGCCGCGGGGGCGGCGCTCTATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACG                                   <  NB501016:282:H2V7GAFX2:1:11202:22914:11485/151‑1 (MQ=60)
                                                                                                                  TTGGTTTGCGGCGCCGGT‑‑GACTTCGC‑‑‑‑GCGCCGCGCGGGGGGCGGGCTATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGT                        <  NB501016:282:H2V7GAFX2:2:11102:3911:5445/150‑1 (MQ=60)
                                                                                                                             CGCCTGTGAGA‑‑TCGC‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCG            <  NB501016:282:H2V7GAFX2:2:21209:26236:16214/151‑1 (MQ=60)
                                                                                                                                      GA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCC   >  NB501016:282:H2V7GAFX2:1:11112:7376:6811/1‑151 (MQ=60)
                                                                                                                                      GA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGC    >  NB501016:282:H2V7GAFX2:4:21408:26512:13928/1‑150 (MQ=60)
                                                                                                                                       A‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCGCTTCCATGCCCCTCAATGCTGCCACCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCAC  >  NB501016:282:H2V7GAFX2:4:21410:1184:2572/1‑151 (MQ=60)
                                                                                                                                       A‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCAC  >  NB501016:282:H2V7GAFX2:4:21409:26814:2566/1‑151 (MQ=60)
                                                                                                                                       |                                                                                                                                                            
GCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGT‑‑GA‑‑TCGA‑‑‑‑GCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCAC  >  NC_002947_CJ‑RC/1070115‑1070398

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: ‑