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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,294,462 G→T 49.1% S261S (TCC→TCA)  nac ← DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,294,4620GT49.1% 15.7 / 100.0 92S261S (TCC→TCA) nacDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base G (32/14);  new base T (21/24);  total (53/39)
Fisher's exact test for biased strand distribution p-value = 3.43e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAACGCGCG  >  minE/1294399‑1294519
                                                               |                                                         
tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:1726422/69‑1 (MQ=255)
tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:1141889/69‑1 (MQ=255)
tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:1655149/69‑1 (MQ=255)
tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:2845626/69‑1 (MQ=255)
tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:873604/69‑1 (MQ=255)
tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:837029/69‑1 (MQ=255)
tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:782788/69‑1 (MQ=255)
tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:2934565/69‑1 (MQ=255)
tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:1480796/69‑1 (MQ=255)
tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:490750/69‑1 (MQ=255)
 gcctgtgcctgtGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:965572/68‑1 (MQ=255)
        cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGt                                                <  1:3282400/67‑1 (MQ=255)
              gCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGt                                                >  1:3127008/1‑61 (MQ=255)
              gCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGt                                                >  1:2555794/1‑61 (MQ=255)
              gCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGt                                         <  1:1328243/68‑1 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAAt                                             >  1:883800/3‑61 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGAc                                      >  1:110306/3‑68 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:47985/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:377712/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:2447406/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:3027479/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:764479/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:2558939/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:2380009/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:92250/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:2291214/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:2282731/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:1866301/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:1068813/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:1520693/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:1251145/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:1707178/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:1780949/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGAGGTAATGCGTGACa                                     >  1:3345797/3‑69 (MQ=255)
                 acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTAATTGAAGGAGTGGTAATGCGTGACa                                     >  1:47611/3‑69 (MQ=255)
                 acaaGTTTGATCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                                     >  1:1473342/3‑69 (MQ=255)
                   aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc                                   >  1:1248245/1‑69 (MQ=255)
                   aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc                                   >  1:120414/1‑69 (MQ=255)
                   aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc                                   >  1:2136766/1‑69 (MQ=255)
                   aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc                                   >  1:3286672/1‑69 (MQ=255)
                   aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc                                   >  1:1618141/1‑69 (MQ=255)
                     gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTaa                                              >  1:1253904/1‑56 (MQ=255)
                     gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACa                                     >  1:823143/1‑65 (MQ=255)
                     gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                                 >  1:2886081/1‑69 (MQ=255)
                     gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                                 >  1:1896914/1‑69 (MQ=255)
                     gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                                 >  1:1448510/1‑69 (MQ=255)
                     gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                                 >  1:921735/1‑69 (MQ=255)
                     gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                                 >  1:2942254/1‑69 (MQ=255)
                     gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                                 >  1:572479/1‑69 (MQ=255)
                     gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                                 >  1:92052/1‑69 (MQ=255)
                      ttCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                                 >  1:1636824/1‑68 (MQ=255)
                       tCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                                      <  1:2741625/46‑1 (MQ=255)
                                   gTAAATTTAAGGACAAAGAGAGACTCAT‑TAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:296263/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:11547/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:3389385/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:296596/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:371869/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:376162/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:1433109/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:1421030/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:590118/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:675859/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:1200065/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:2146718/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:2346250/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:2392564/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:2298872/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:2194923/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:2170328/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:2156678/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:2772046/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:2822231/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:293660/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:1516643/69‑1 (MQ=255)
                                    tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:3108918/69‑1 (MQ=255)
                                       aTTTAAGGACAAAGAGAGAGTCATTGAAGGAGTTGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:2080230/66‑1 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTAc                        >  1:2387542/1‑58 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACAt              >  1:471581/1‑68 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACAt              >  1:260034/1‑68 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa             >  1:1820371/1‑69 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa             >  1:1877396/1‑69 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa             >  1:1497334/1‑69 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa             >  1:2327394/1‑69 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa             >  1:536392/1‑69 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa             >  1:1576780/1‑69 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa             >  1:465831/1‑69 (MQ=255)
                                         ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa             >  1:1528204/1‑69 (MQ=255)
                                                    gagagaCTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAAcgcgcg  >  1:882131/1‑69 (MQ=255)
                                                    gagagaCTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAAcgcgcg  >  1:2628413/1‑69 (MQ=255)
                                                    gagagaCTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAAcgcgcg  >  1:396063/1‑69 (MQ=255)
                                                      gagaCTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATaacg          >  1:1848551/1‑59 (MQ=255)
                                                           tCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc                  <  1:1052129/46‑1 (MQ=255)
                                                               |                                                         
TGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATAACGAACGCGCG  >  minE/1294399‑1294519

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A