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 1,896,246 C→A 40.9% intergenic (‑199/‑33) amiC ← / → argA N‑acetylmuramoyl‑L‑alanine amidase/fused acetylglutamate kinase homolog (inactive) and amino acid N‑acetyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,896,2460CA40.9% 59.2 / 76.3 88intergenic (‑199/‑33)amiC/argAN‑acetylmuramoyl‑L‑alanine amidase/fused acetylglutamate kinase homolog (inactive) and amino acid N‑acetyltransferase
Reads supporting (aligned to +/- strand):  ref base C (6/46);  new base A (23/13);  total (29/59)
Fisher's exact test for biased strand distribution p-value = 4.37e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

TAAAAAAGTCGCTCTCGCATAAAATTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAGGAACGTAAAACCGAGTTGGTCGAGGGA  >  minE/1896182‑1896314
                                                                |                                                                    
tAAAAAAGTCGCTCTCGCATAAAATTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAAt                                                                  >  1:2193017/1‑69 (MQ=255)
tAAAAAAGTCGCTCTCGCATAAAATTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAAt                                                                  >  1:237518/1‑69 (MQ=255)
tAAAAAAGTCGCTCTCGCATAAAATTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAAt                                                                  >  1:7169/1‑69 (MQ=255)
                  aTAAAATTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCaa                                                 <  1:1138380/68‑1 (MQ=255)
                  aTAAAATTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCaa                                                 <  1:870644/68‑1 (MQ=255)
                     aaaTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAagag                                             >  1:3341205/1‑69 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATTCACTAATTTCTAATAATCATGCAAAGAgg                                            <  1:1112354/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCTAAGAgg                                            <  1:5281/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:367152/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:757939/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:2190070/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:78814/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:1762718/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:79125/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:688005/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:573009/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:3132045/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:3428202/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:3398922/68‑1 (MQ=255)
                       aTTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCCAATAATCATGCAAAGAgg                                            <  1:588293/68‑1 (MQ=255)
                        tttACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:1594776/67‑1 (MQ=255)
                             acTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGcc                                      <  1:2017986/68‑1 (MQ=255)
                             acTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGcc                                      <  1:185149/68‑1 (MQ=255)
                             acTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGcc                                      <  1:422390/68‑1 (MQ=255)
                             acTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGcc                                      <  1:901229/68‑1 (MQ=255)
                             acTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGcc                                      <  1:729464/68‑1 (MQ=255)
                              cTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGcc                                      <  1:2951470/67‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:3225083/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:2287565/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:2332967/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:2083175/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:2141384/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:828250/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:1741417/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:1129619/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:1588617/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:870238/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:1395572/59‑1 (MQ=255)
                                tGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTg                                   >  1:2623022/1‑68 (MQ=255)
                                 gCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAgg                                            <  1:2637921/58‑1 (MQ=255)
                                      cTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAgg                            <  1:994668/69‑1 (MQ=255)
                                      cTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAgg                            <  1:1260932/69‑1 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGaataat                                                        >  1:1588047/1‑40 (MQ=38)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGGAAAGAGgtgtac                                       >  1:1093319/1‑55 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAgg                            >  1:2880593/1‑68 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1382469/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1376175/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:3150829/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:467111/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1108904/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1060929/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:2915688/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1875264/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:2788222/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1596636/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1020622/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1601468/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:2325587/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:814523/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1658093/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1818777/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:2179720/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGa                           >  1:1989445/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGAAAAGGa                           >  1:2223957/1‑69 (MQ=255)
                                       tGCAAAAAAACAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGAAAAGGa                           >  1:2220071/1‑69 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAATGAACGt                       <  1:2733689/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:606795/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:2372540/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:103329/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:1460670/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:3050808/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:2986707/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:2981242/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:2766286/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:151664/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:1695043/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:2533620/69‑1 (MQ=255)
                                           aaaaaaCAGAATAAAAATACAATAATTTCGAATAATCATGCAAAGAGGTGTACCGTGGTAAAGGAACGt                       <  1:1977891/69‑1 (MQ=255)
                                             aaaaCAGAATAAAAATACACTAATTTCGAATAATCATGCa                                                  <  1:2267348/40‑1 (MQ=255)
                                             aaaaCAGAATAAAAATACACTAATTTCGAATAATCATGCa                                                  <  1:1790863/40‑1 (MQ=255)
                                             aaaaCAGAATAAAAATACACTAATTTCGAATAATCATGCa                                                  <  1:2569800/40‑1 (MQ=255)
                                             aaaaCAGAATAAAAATACACTAATTTCGAATAATCATGCa                                                  <  1:633245/40‑1 (MQ=255)
                                                  aGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAGGAACGTAAAACCg                <  1:1657568/69‑1 (MQ=255)
                                                  aGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAGGAACGTAAAACCg                <  1:123818/69‑1 (MQ=255)
                                                  aGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAGGAACGTAAAACCg                <  1:934953/69‑1 (MQ=255)
                                                     aTAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAGGAACGTAAAACCGAGt             <  1:3268196/69‑1 (MQ=255)
                                                     aTAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAGGAACGTAAAACCGAGt             <  1:1335489/69‑1 (MQ=255)
                                                        aaaaTACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAGGAACGTAAAACCGAGTTgg          >  1:3192545/1‑69 (MQ=255)
                                                                cTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAGGAACGTAAAACCGAGTTGGTCGAGGGa  <  1:444332/69‑1 (MQ=255)
                                                                |                                                                    
TAAAAAAGTCGCTCTCGCATAAAATTTACACTTGCACCCTGCGAAAAAACAGAATAAAAATACACTAATTTCGAATAATCATGCAAAGAGGTGTGCCGTGGTAAAGGAACGTAAAACCGAGTTGGTCGAGGGA  >  minE/1896182‑1896314

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A