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 F1 I1 R1 150 26.0 2053212 90.0% 1847890 107.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 1,492,953 T→G S201A (TCA→GCA)  pdhB → dihydrolipoamide acetyltransferase (E2) component of pyruvate dehydrogenase complex

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604791,492,9530TG100.0% 14.2 / NA 6S201A (TCA→GCA) pdhBdihydrolipoamide acetyltransferase (E2) component of pyruvate dehydrogenase complex
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (3/3);  total (3/3)

CGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGTTGCTGCTGATCCTGGAAGGCGCCGCCGCATCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCCGCCGCTGGCG  >  AM260479/1492861‑1493082
                                                                                            |                                                                                                                                 
cgcAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCAccggctccggct                                                                                          >  2:536717/1‑134 (MQ=255)
       cggcgTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAgcg                                                                                   <  2:834286/134‑1 (MQ=255)
                                                                           tGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCgccg               >  2:47692/1‑134 (MQ=255)
                                                                                 gcgcCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGgccgcc         <  1:536717/134‑1 (MQ=255)
                                                                                  cgccgccgcAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCg                                             <  1:838897/97‑1 (MQ=255)
                                                                                  cgccgccgcAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCg                                             >  2:838897/1‑97 (MQ=255)
                                                                                         gcagcaGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCCGCCGCTGGCg  >  2:540946/1‑133 (MQ=255)
                                                                                            |                                                                                                                                 
CGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGTTGCTGCTGATCCTGGAAGGCGCCGCCGCATCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCCGCCGCTGGCG  >  AM260479/1492861‑1493082

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ 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
GGTGACGCTGGAGTCCGACAAGGCCACCATGGACGTGCCGTCGCCGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGTTGCTGCTGATCCTGGAAGGCGCCGCCGCATCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCCGCCGCTGGCGTAACCGGC  >  AM260479/1492817‑1493090
                                                                                                                                        |                                                                                                                                         
GGTGACGCTGGAGTCCGACAAGGCCACCATGGACGTGCCGTCGCCGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGC                                                                                                                              <  GWNJ‑0478:712:GW2002102894th:2:2101:17140:92614/150‑1 (MQ=60)
                                                                                         cggagatgtgtataagagacagGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCA                                      <  GWNJ‑0478:712:GW2002102894th:2:2205:17628:85953/127‑1 (MQ=60)
                                                                                                                        GGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCCGCCGCTGGCGTAAC      >  GWNJ‑0478:712:GW2002102894th:2:1109:14547:96931/1‑150 (MQ=60)
                                                                                                                            GGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCCGCCGCTGGCGTAACCGGC  <  GWNJ‑0478:712:GW2002102894th:2:2103:19961:58880/150‑1 (MQ=60)
                                                                                                                                        |                                                                                                                                         
GGTGACGCTGGAGTCCGACAAGGCCACCATGGACGTGCCGTCGCCGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGTTGCTGCTGATCCTGGAAGGCGCCGCCGCATCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCCGCCGCTGGCGTAACCGGC  >  AM260479/1492817‑1493090

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑