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
A4 F50 I2 R1 104 44.1 1376607 98.9% 1361464 150.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,222,366 T→C V61A (GTG→GCG)  dld → D‑lactate dehydrogenase, FAD‑binding, NADH independent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,222,3660TC97.7% 114.4 / ‑6.6 43V61A (GTG→GCG) dldD‑lactate dehydrogenase, FAD‑binding, NADH independent
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (11/31);  minor base G (1/0);  total (12/31)
Fisher's exact test for biased strand distribution p-value = 2.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.29e-01

TTGAATGAACTTGCTCGTCTGGTGGGTTCTTCACACCTGCTCACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGTGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAGCACCCTGCGTCTCGACAAGCTGCACGTTC  >  NC_000913/2222221‑2222512
                                                                                                                                                 |                                                                                                                                                    
ttGAATGAACTTGCTCGTCTGGTGGGTTCTTCACACCTGCTCACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCt                                                                                                                                                   >  2:455803/1‑149 (MQ=255)
  gaatgaaCTTGCTCGTCTGGTGGGTTCTTCACACCTGCTCACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGaaa                                                                                                                                               <  1:162130/151‑1 (MQ=255)
   aatgaaCTTGCTCGTCTGGTGGGTTCTTCACACCTGCTCACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAg                                                                                                                                              <  1:96317/151‑1 (MQ=255)
   aatgaaCTTGCTCGTCTGGTGGGTTCTTCACACCTGCTCACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCGGaaa                                                                                                                                               >  1:8890/1‑150 (MQ=255)
      gaaCTTGCTCGTCTGGTGGGTTCTTCACACCTGCTCACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCGGGAAg                                                                                                                                              >  1:209688/1‑148 (MQ=255)
                     gtggGTTCTTCACACCTGCTCACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACa                                                                                                                            <  2:304838/151‑1 (MQ=255)
                                 cacCTGCTCACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTg                                                                                                                 <  1:105707/150‑1 (MQ=255)
                                    cTGCTCACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGGCAAAAATATTCTGAt                                                                                                               >  2:147343/1‑149 (MQ=255)
                                         cACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGCCGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGgcc                                                                                                        <  1:125531/151‑1 (MQ=255)
                                         cACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGgcc                                                                                                        <  2:95718/151‑1 (MQ=255)
                                          aCCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAACCTGCGGCACCGCCGACAAAATTATTCTGATGCAGgcc                                                                                                        >  2:69327/1‑150 (MQ=255)
                                            cGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGgccg‑cc                                                                                                    <  2:121175/151‑1 (MQ=255)
                                             gATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCCGTTGAAGTCTGCGGCCACCCCGGCCAAAATATTCTTATTGAGgccg‑cc                                                                                                    >  1:341938/1‑150 (MQ=255)
                                                               cGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAACCTGCGTCACCGCCGACAAAATTATTTTGATGCAGGCCG‑CCCATACAGGCCTGAcc                                                                                     >  2:226248/1‑147 (MQ=255)
                                                                   aTCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATc                                                                             <  2:493614/151‑1 (MQ=255)
                                                                          gggCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑cc                                                                      <  2:540258/150‑1 (MQ=255)
                                                                              ttCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAAc                                                                  <  1:430759/150‑1 (MQ=255)
                                                                                ccGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACgg                                                                <  2:534615/150‑1 (MQ=255)
                                                                                ccGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACg                                                                 <  2:168262/149‑1 (MQ=255)
                                                                                       ggTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACg                                                           <  1:533766/148‑1 (MQ=255)
                                                                                       ggTAAGGGCGACGCGCTGGCTGTCGTTTCCCCTGGCTCCCTCCTAGAATTGTGGCGGGCGCTGAAAGCTTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACg                                                           <  1:657615/148‑1 (MQ=255)
                                                                                           aGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTAt                                                      <  1:201095/149‑1 (MQ=255)
                                                                                           aGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGa                                                    <  2:338361/151‑1 (MQ=255)
                                                                                                gACGCGCTGGCTGTCTTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATcg                                                 <  2:233160/149‑1 (MQ=255)
                                                                                                gACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTTAAAACCTGCGTCACCGCCGACAAAATTATTCTGATGCAAGCCG‑CCAATACAAGCCTGACCGAAGGATCGACG‑CCCAACGGTAAACATTAttaac                                                  >  2:3217/1‑144 (MQ=255)
                                                                                                gACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATcgc                                                <  2:217394/150‑1 (MQ=255)
                                                                                                   gcgcTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATg                                            <  2:343398/151‑1 (MQ=255)
                                                                                                        ggctgTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGtt                                       <  2:349001/151‑1 (MQ=255)
                                                                                                        ggctgTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGt                                        <  2:55212/150‑1 (MQ=255)
                                                                                                          ctgTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTa                                      <  1:398131/150‑1 (MQ=255)
                                                                                                          ctcttgTTTTCCCTGCCTCACTACTAGAATTGTGGCGGGCGCTGAAGGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGt                                        <  1:138749/143‑1 (MQ=255)
                                                                                                           tgTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCCCCGACAAAATTATTTTTATGCAGGCCGCCCAAAACA‑GCCTGACCGAAGGGGCGACGCCCAAACGG‑AACGATTATTATTCCGACGGCGTTat                                     >  1:677877/1‑150 (MQ=255)
                                                                                                                 tttCCCTGGCTCACTACTAGAATTGTGGCGGGGGCTGCAAGCCTTCGTCACCCCCGGCCACATTATTTTTTTGAAAGCCG‑CCCAAAAAAGCCCGATCGCAAGAACGACG‑CCCAAAGGAAAACATTATGGTCGCGGTTTCGtttttttcaa                               >  1:579384/1‑142 (MQ=255)
                                                                                                                 tttCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAg                               <  2:114460/150‑1 (MQ=255)
                                                                                                                  ttCCCTGGCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAGc                              <  1:170295/150‑1 (MQ=255)
                                                                                                                        ggCTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAGCACCCt                         <  1:289516/149‑1 (MQ=255)
                                                                                                                          cTCACTACTAGAATTGTGGCGGGCGCTGAAAGCCTGCTCCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAGCACCCt                         <  2:418920/147‑1 (MQ=255)
                                                                                                                                actaGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAGCACCCTGCGTCTCGAc               <  1:384254/151‑1 (MQ=255)
                                                                                                                                   aGAATTGTGGCGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAGCACCCTGCGTCTCGACa              <  1:631567/149‑1 (MQ=255)
                                                                                                                                     aaTTGTGGCGGGCGCTGAAAGCCGGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAGCACCCTGCGTCTCGACAAGCt          <  1:163802/151‑1 (MQ=255)
                                                                                                                                     aaTTGTGGCGGGCGCCGAAAACCCGCGTCACCGCCCCCAAAAATATTTTGATGCAGGCCG‑CCAATACAAGGCCGGCCGAAGGATCGGCG‑CCAAACGGGAACGATTATTATCCCGATGTCCTTATCATCACCACCCCGCGCCTCGGCaaa            >  1:270884/1‑148 (MQ=255)
                                                                                                                                             cGGGCGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAGCACCCTGCGTCTCGACAAGCTGCACGTTc  >  1:294129/1‑151 (MQ=255)
                                                                                                                                              gggCGCTGAAAGCTTGCTTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAGCACCCTGCGTCTCGACAAGCTGCACGTTc  <  1:341587/150‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                    
TTGAATGAACTTGCTCGTCTGGTGGGTTCTTCACACCTGCTCACCGATCCCGCAAAAACGGCCCGCTATCGCAAGGGCTTCCGTTCTGGTCAGGGCGACGCGCTGGCTGTCGTTTTCCCTGGCTCACTACTAGAATTGTGGCGGGTGCTGAAAGCCTGCGTCACCGCCGACAAAATTATTCTGATGCAGGCCG‑CCAATACAGGCCTGACCGAAGGATCGACG‑CCAAACGGTAACGATTATGATCGCGATGTCGTTATCATCAGCACCCTGCGTCTCGACAAGCTGCACGTTC  >  NC_000913/2222221‑2222512

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A