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
A2 F80 I1 R1 130 60.2 1467357 98.1% 1439477 216.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,953,402 A→G N234S (AAC→AGC)  cmoA → carboxy‑S‑adenosyl‑L‑methionine synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,953,4020AG96.8% 104.6 / ‑6.0 31N234S (AAC→AGC) cmoAcarboxy‑S‑adenosyl‑L‑methionine synthase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (12/18);  total (12/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GCGCGCTGGTGCTTTCGGAAAAATTCAGTTTCGAAGATGCCAAAGTTGGTGAACTGTTGTTCAACATGCACCACGACTTTAAACGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAACTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGGTTGTTTAAGCAGTGGTCAAATGCGGTGGAGTTTCTACCTGAAATTAAACCGTATCGTCTTGATTTATTGCAT  >  NC_000913/1953174‑1953624
                                                                                                                                                                                                                                    |                                                                                                                                                                                                                              
gcgcgcTGGTGCTTTCGGAAAAATTCAGTTTCGAAGATGCCAAAGTTGGTGAACTGTTGTTCAACATGCACCACGACTTTAAACGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCAc                                                                                                                                                                                                                     >  1:300015/1‑240 (MQ=255)
      tGGTGCTTTCGGAAAAATTCAGTTTCGAAGATGCCAAAGTTGGTGAACTGTTGTTCAACATGCACCACGACTTTAAACGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACtggtg                                                                                                                                                                                                                <  1:144152/239‑1 (MQ=255)
            tttCGGAAAAATTCAGTTTCGAAGATGCCAAAGTTGGTGAACTGTTGTTCAACATGCACCACGACTTTAAACGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTaa                                                                                                                                                                                                         <  1:595671/240‑1 (MQ=255)
                      aTTCAGTTTCGAAGATGCCAAAGTTGGTGAACTGTTGTTCAACATGCACCACGACTTTAAACGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGa                                                                                                                                                                                               <  1:601148/240‑1 (MQ=255)
                          aGTTTCGAAGATGCCAAAGTTGGTGAACTGTTGTTCAACATGCACCACGACTTTAAACGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACtggt                                                                                                                                                                                                                 <  2:412657/218‑1 (MQ=255)
                                                        ttgttCAACATGCACCACGACTTTAAACGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGa                                                                                                                                                                                               <  2:457734/206‑1 (MQ=255)
                                                                         cGACTTTAAACGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAatcat                                                                                                                                            >  1:491187/1‑240 (MQ=255)
                                                                          gACTTTAAACGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAatcat                                                                                                                                            >  1:49386/1‑239 (MQ=255)
                                                                                 aaCGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTcaca                                                                                                                                    <  1:373669/240‑1 (MQ=255)
                                                                                 aaCGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTcaca                                                                                                                                    <  1:45656/240‑1 (MQ=255)
                                                                                              ttACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACg                                                                                                                       >  1:7641/1‑240 (MQ=255)
                                                                                                          ggAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCa                                                                                                            <  1:482739/239‑1 (MQ=255)
                                                                                                            agaTCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTCACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCTGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAatc                                                                                                                                              <  2:137675/203‑1 (MQ=255)
                                                                                                                        aGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCa                                                                                             <  1:276535/240‑1 (MQ=255)
                                                                                                                          cgcAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAgc                                                                                           >  1:690308/1‑240 (MQ=255)
                                                                                                                                       aaaaCGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAgcagcagca                                                                              <  2:491178/240‑1 (MQ=255)
                                                                                                                                          aCGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACgg                                                                           <  1:29216/240‑1 (MQ=255)
                                                                                                                                           cGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACggg                                                                          >  1:364534/1‑240 (MQ=255)
                                                                                                                                              gATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAatc                                                                                                                                              <  2:206826/169‑1 (MQ=255)
                                                                                                                                                     aCCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGGTTGTTTAAGc                                                                >  1:110514/1‑240 (MQ=255)
                                                                                                                                                      ccGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGGTTGTTTAAGCa                                                               <  1:90812/240‑1 (MQ=255)
                                                                                                                                                        gATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCCGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGcgcg                                                                                        <  1:354878/213‑1 (MQ=255)
                                                                                                                                                               tGGAAACCCATAAAGCACGCCTGCATAACGCCGGGTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCaca                                                                                                                                                  >  1:276292/1‑146 (MQ=255)
                                                                                                                                                                                cGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGTTTGTTTAAGCAGTGGTCAAATGCGGTGGAGTTTc                                        >  2:580655/1‑237 (MQ=255)
                                                                                                                                                                                cGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGGTTGTTTAAGCAGTGGTCAAATGCGGTGGAGTTTCTAc                                     >  1:45710/1‑240 (MQ=255)
                                                                                                                                                                                cGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGGTTGTTTAAGCAGTGGTCAAATGCGGTGGAGTTTCTAc                                     >  2:702274/1‑240 (MQ=255)
                                                                                                                                                                                             ccGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGGTTGTTTAAGCAGTGGTCAAATGCGGTGGAGTTTCTAcc                                    <  2:432026/228‑1 (MQ=255)
                                                                                                                                                                                                         aTAGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGGTTGTTTAAGCAGTGGTCAAATGCGGTGGAGTTTCTACCTGAAATTAAACCGTATCGTCTTg             <  1:76703/239‑1 (MQ=255)
                                                                                                                                                                                                           aGTGAGCTGTGGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGGTTGTTTAAGCAGTGGTCAAATGCGGTGGAGTTTCTACCTGAAATTAAACCGTATCGTCTTGAtt          >  2:417851/1‑240 (MQ=255)
                                                                                                                                                                                                                  tgtgGTTCCAGTGCTTTAACTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACgg                                                                           <  2:570020/168‑1 (MQ=255)
                                                                                                                                                                                                                   gtgGTTCCAGTGCTTTAGCTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGGTTGTTTAAGCAGTGGTCAAATGCGGTGGAGTTTCTACCTGAAATTAAACCGTATCGTCTTGATTTATTGCAt  <  1:569700/240‑1 (MQ=255)
                                                                                                                                                                                                                                    |                                                                                                                                                                                                                              
GCGCGCTGGTGCTTTCGGAAAAATTCAGTTTCGAAGATGCCAAAGTTGGTGAACTGTTGTTCAACATGCACCACGACTTTAAACGTGCCAACGGTTACAGCGAACTGGAGATCAGCCAGAAGCGCAGCATGCTGGAAAACGTGATGCTGACCGATTCCGTGGAAACCCATAAAGCACGCCTGCATAACGCCGGTTTTGAGCATAGTGAGCTGTGGTTCCAGTGCTTTAACTTTGGTTCACTGGTGGCATTAAAAGCAGAGGACGCTGCATGATCGACTTTGGTAACTTTTATTCTCTGATTGCCAAAAATCATCTTTCACACTGGCTCGAAACGCTGCCCGCGCAGATTGCTAACTGGCAGCGCGAGCAGCAGCACGGGTTGTTTAAGCAGTGGTCAAATGCGGTGGAGTTTCTACCTGAAATTAAACCGTATCGTCTTGATTTATTGCAT  >  NC_000913/1953174‑1953624

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A