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 F17 I0 R1 155 84.1 1797446 90.9% 1633878 230.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 75,091 G→T 36.0% D130E (GAC→GAA)  thiB ← thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091375,0910GT36.0% 26.7 / 3.2 25D130E (GAC→GAA) thiBthiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base G (3/13);  new base T (7/2);  total (10/15)
Fisher's exact test for biased strand distribution p-value = 8.95e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAACGCCATCTTCCAGCGCCACCAGTTTCAGTT  >  NC_000913/74875‑75329
                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                  
gCCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGTC‑GGGGTTTT‑ACGTTTTTTTTTTTCTT‑TAACGaaatgcaaggag                                                                                                                                                                                                                              >  2:751377/1‑228 (MQ=255)
gCCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTT‑TGTTTTTTTTTTGTTAT‑AAAAAAAgggaaagaag                                                                                                                                                                                                                              >  1:244461/1‑231 (MQ=255)
gCCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTT‑TAGTTTTTTCTTTTTCT‑TAACAAAAGCGCAGTAg                                                                                                                                                                                                                              >  2:68849/1‑238 (MQ=255)
        cTTCCCCCCAGTTTTTGTTGCCCGTGCCCGTTTTTTCCGCCATTTTCGCCCGGGTTGGGGGGGCGTCTTCGCCATAGATTTTTTGCACCAATAGCAACAGCCCCAGCCCGGGTGTACTGGTGCGCGGATCCTGATAAATCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCa                                                                                                                                                                                                                     <  1:689352/239‑1 (MQ=255)
         ttCGCTCCAGCTTTGGGTTACTGGCACCGTTTTCGTCGCCAGTTGCTGCCGGGCTGGGGGGGCGTCATGACCAAAGACTTTTTGCATCCATAGCAACAGCCCCATCCCCGGTTTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCa                                                                                                                                                                                                                     <  2:62529/238‑1 (MQ=255)
          tCGCTCCCGCCTTGGGGCACGTTGCCCTTTTTCTTCGCCAGTTGCTGCAGGGCTTGGGGGGCGTCATCGCCTTAGACTTTTTGCACCCATAGCAACAGCCCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCaaa                                                                                                                                                                                                                   <  2:377130/239‑1 (MQ=255)
          tCGCTCCAGCCTTTGGTGACCGTGACCGTTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGCC‑GGGGTTTT‑CCTTTTTTTATTTTTAT‑AAACAAAAGCGAAGTGGtcatcatcaca                                                                                                                                                                                                                   >  2:321225/1‑237 (MQ=255)
                        ggTGACCGTGACCGTTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGCGTTTT‑TAGTTTTTTTTTTTCAT‑ATACAAAAAGGCAGTAGTCAATATTACACTGTACGaaacggg                                                                                                                                                                                                     >  2:20953/1‑235 (MQ=255)
                             ccgtgaccgtTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTT‑CAGTTTGTTTTTTTCTT‑AAAACAAGGCGGAGTAGCCCTAATCAACAGGGAAGAAAAAGTCatta                                                                                                                                                                                                >  2:823010/1‑239 (MQ=255)
                                                                     ggCGTCAGCGCCATAGCCTTTTGGCATCCATAGCAACAGCCCCAGCCCCGGTGTACGGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCcaca                                                                                                                                                        <  2:244461/238‑1 (MQ=255)
                                                                                                   tAGCAACAGCCCCGGCCCGGGTGTACTGGTGCGCGGATCCTGATAAACCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTg‑g                                                                                                                       <  2:743231/239‑1 (MQ=255)
                                                                                                       acacgACCCAGCCCGGGTGTATGGGTGCCCGGATCCTGATAAACCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTg‑gcggc                                                                                                                   <  2:264522/235‑1 (MQ=255)
                                                                                                            aCCCAGCCCCGGTGTACTGGTGCTCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGATTTTT‑CAGTTTGTTCTTTTCAT‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCCGGAAAGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑GCAACAGTCCGGTTTTACTT‑GAGGCGACTa                                                                                                              >  2:697796/1‑239 (MQ=255)
                                                                                                                 gCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTT‑CAGTTTTTTTTTGTCTT‑AAACGAAGGCGAAGTAGCCCTAATCAAACGGTACGAAAATGTCATTATTCCCG‑CCGCCGGGGACGCTAACGGCATCCCCCGCCACACCCCTTTTTG‑CCAAAAACCCGGCTTTATTG‑GCGGCGGCTTACAgg                                                                                                         >  2:571791/1‑239 (MQ=255)
                                                                                                                     gggTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAg                                                                                                                                      <  2:657677/206‑1 (MQ=255)
                                                                                                                               ggtgggggATTCTTATAAATCCCCCGCAAGTTTTGATCGCTCCCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGccc                                                                                           <  2:233420/233‑1 (MQ=255)
                                                                                                                                  cgcgGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTT‑TAGTTTTTTTTTTTCCTAAAACAAAGGGGAGGAGCCCATAATCAAACGTGAGGCAAG‑GTCATTTTTTCAGACCCCCGGGAAGGTAAACGCCA‑CCGCCTCCACCCCCCCTTTGGTCAAAAAGCCGGGTTTTATTGTGCCGCG‑CTAAAAGATTGTTATACAcccaa                                                                                          >  1:231752/1‑236 (MQ=255)
                                                                                                                                          cttaTAACTCCCCCTCCATTTTTGACCGCTCTCAACCAGTTTTTTCAGGCTTGGTGGC‑GGTTTTTT‑CAGTTTGTTTTTGTCAT‑AAACGAAGGCGAAGTAGCCAAAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACAt                                                                                <  1:20953/236‑1 (MQ=255)
                                                                                                                                                         cagttttttctcctttcctgctaGTTCTTTCATG‑TTTGGGGC‑CGGTTTTTCCATGTTGTTCTTGTAAG‑AACCGAAGGCGAAGTAGCCATAACCAATCGGTACGAAAGTGTAATTTTTCCAG‑CCGCCCGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGtttt                                                                 <  1:685294/217‑1 (MQ=255)
                                                                                                                                                                tGATCGCTCTCACCCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCAAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTc                                                          <  2:439629/239‑1 (MQ=255)
                                                                                                                                                                                              tttgGG‑GGTTTTTT‑CTGTTTTTTTTTTTCAT‑AACCAAAGGGGAAGTAGCAATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAACGcc                            <  1:823010/237‑1 (MQ=255)
                                                                                                                                                                                                        ttttt‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAATTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAACGCCATCTTCCa                    <  2:574853/238‑1 (MQ=255)
                                                                                                                                                                                                           tt‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACCGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCCTCCGTCGACGGTTGATAAGCGCAAAGCCATCTTCCAgcg                 >  1:753735/1‑238 (MQ=255)
                                                                                                                                                                                                            t‑CAGTTTGTTCTGTTAAA‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTTTTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAACGCCATCTTCCAGCGcc               <  2:231752/239‑1 (MQ=255)
                                                                                                                                                                                                                     tttttGTCAT‑AAAGTAAGGCAAGTTAGGTATAATCAAACGGTACGAAATTTGCATTATCCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAACGCCATCTTCCAGCGCCACCAGttt       <  1:279749/236‑1 (MQ=255)
                                                                                                                                                                                                                          gTCAT‑GAACGAAGGCGAAGTGGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAACGCCATCTTCCAGCGCCACCAGTTTCAGtt  <  2:594890/239‑1 (MQ=255)
                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                  
GCCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTT‑CAGTTTGTTCTTGTCAT‑AAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAG‑CCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGG‑CAAACAGTCCGGTTTTACTG‑GCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAACGCCATCTTCCAGCGCCACCAGTTTCAGTT  >  NC_000913/74875‑75329

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A