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
A0 F0 I1 R1 149 26.7 2337422 87.5% 2045244 105.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 160,050 +C coding (314/939 nt) h16_A0146 → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM260479160,0481.C100.0% 21.8 / NA 7R104R (CGA→CGC) h16_A0146conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (3/4);  total (3/4)

CGCAGGGCGCGACCGAGATGGCGTCGGGCAGTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCCGGCGGGCCGCAGGGCGGCGTCGATGGCGTGGGGTACGA‑CCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGGCAGCCGCTACCGG  >  AM260479/159931‑160147
                                                                                                                      |                                                                                                   
cGCAGGGCGCGACCGAGATGGCGTCGGGCAGTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCCGGCGGGCCGCAGGGCGGCGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGcg                                                                                      <  1:469332/134‑1 (MQ=255)
                              gTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCCGGCGGGCCGCAGGGCGGCGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGc                                                        >  1:461189/1‑134 (MQ=255)
                                                                                 gcggGCCGCAGGGCGGCGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGGCAGCCGCTAc     >  2:135051/1‑134 (MQ=255)
                                                                                    ggCCGCAGGGCGGCGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGGCAGCCGCTACCgg  <  1:135051/134‑1 (MQ=255)
                                                                                    ggCCGCAGGGCGGCGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGGCAGCCGCTACCgg  <  1:313294/134‑1 (MQ=255)
                                                                                                                ctACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGcc                                     >  1:360327/2‑71 (MQ=255)
                                                                                                                ctACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGcc                                     <  2:360327/70‑1 (MQ=255)
                                                                                                                      |                                                                                                   
CGCAGGGCGCGACCGAGATGGCGTCGGGCAGTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCCGGCGGGCCGCAGGGCGGCGTCGATGGCGTGGGGTACGA‑CCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGGCAGCCGCTACCGG  >  AM260479/159931‑160147

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CCGCAGGGCGCGACCGAGATGGCGTCGGGCAGTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCCGGCGGGCCGCAGGGCGGCGTCGATGGCGTGGGGTACGA‑CCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGGCAGCCGCTACCGGCTGGCGGTCGAAACCCGCGTGCTGTGGTTCCGCTTTGCCTTCCA  >  AM260479/159930‑160191
                                                                                                                         |                                                                                                                                             
CCGCAGGGCGCGACCGAGATGGCGTCGGGCAGTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCCGGCGGGCCGCAGGGCGGCGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGCGACGATGCACTACGCC                                                                                                                   <  GWNJ‑0478:712:GW2002102894th:2:1210:12006:95089/150‑1 (MQ=60)
                AGATGGCGTCGGGCAGTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCCGGCGGGCCGCAGGGCGGCGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCG                                                                                                   >  GWNJ‑0478:712:GW2002102894th:2:1210:3048:52454/1‑150 (MQ=60)
                                                                                    GGGCCGCAGGGCGGCGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGGCAGCCGCTACCGGCTGGCGGTCGAAACC                               <  GWNJ‑0478:712:GW2002102894th:2:1109:7515:28531/150‑1 (MQ=60)
                                                                                    GGGCCGCAGGGCGGCGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGGCAGCCGCTACCGGCTGGCGGTCGAAACC                               <  GWNJ‑0478:712:GW2002102894th:2:1203:12686:85329/150‑1 (MQ=60)
                                                                                              GCGGCGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgctt                     >  GWNJ‑0478:712:GW2002102894th:2:2106:16437:40446/1‑86 (MQ=60)
                                                                                                  CGTCGATGGCGTGCGCTACGACCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgt                 >  GWNJ‑0478:712:GW2002102894th:2:1204:7756:83239/1‑101 (MQ=60)
                                                                                                                gctacgacCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGGCAGCCGCTACCGGCTGGCGGTCGAAACCCGCGTGCTGTGGTTCCGCTTTGCCTTCC   <  GWNJ‑0478:712:GW2002102894th:2:1104:19120:7556/142‑1 (MQ=60)
                                                                                                                 ctacgacCCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGTCAGCCGttagcggctgccgtcctgctcccagcggttcaggacctgtctcttatacac  >  GWNJ‑0478:712:GW2002102894th:2:1110:3462:56558/8‑99 (MQ=60)
                                                                                                                         |                                                                                                                                             
CCGCAGGGCGCGACCGAGATGGCGTCGGGCAGTGGCGGCGAGGGCAGCGCGGCCAGGCCTGCCGCCGCTGCCGCGCCGTCCGGCGGGCCGCAGGGCGGCGTCGATGGCGTGGGGTACGA‑CCGCCGCCGTCGGCGACGATGCACTACGCCAGCTTCGTCAACGGCGTGCAGAACCCCGACGGCCTGATCCGCTGGGAGCAGGACGGCAGCCGCTACCGGCTGGCGGTCGAAACCCGCGTGCTGTGGTTCCGCTTTGCCTTCCA  >  AM260479/159930‑160191

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑