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
A1 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 1,620,710 C→T intergenic (‑88/‑124) marC ← / → marR predicted transporter/DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,620,7100CT96.5% 260.8 / 0.4 85intergenic (‑88/‑124)marC/marRpredicted transporter/DNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (0/3);  new base T (54/28);  total (54/31)
Fisher's exact test for biased strand distribution p-value = 4.55e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

TTATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTAT  >  W3110S.gb/1620650‑1620779
                                                            |                                                                     
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGGTAGCCTTGTATCGCATTg                                                              >  1:3210383/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:205040/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:2293765/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:3583453/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:1871785/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:3906495/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:3497726/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:2535091/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:53802/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:1741723/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:1687870/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:2546572/1‑70 (MQ=255)
ttATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:1735841/1‑70 (MQ=255)
ttATCAGAGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTg                                                              >  1:2906450/1‑70 (MQ=255)
                taAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCg                                              <  1:213090/70‑1 (MQ=255)
                taAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCg                                              <  1:3937018/70‑1 (MQ=255)
                taAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCg                                              <  1:3115082/70‑1 (MQ=255)
                taAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCg                                              <  1:879749/70‑1 (MQ=255)
                taAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:1672170/71‑1 (MQ=255)
                taAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:148295/71‑1 (MQ=255)
                taAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:3313122/71‑1 (MQ=255)
                taAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:3284737/71‑1 (MQ=255)
                taAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:1142723/71‑1 (MQ=255)
                     ggTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTg                                                   >  1:3704250/1‑60 (MQ=255)
                     ggTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGATCCGATTTa                                         >  1:1314828/1‑70 (MQ=255)
                     ggTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAg                                        >  1:2712242/1‑71 (MQ=255)
                     ggTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAg                                        >  1:219432/1‑71 (MQ=255)
                     ggTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAg                                        >  1:3143070/1‑71 (MQ=255)
                     ggTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAg                                        >  1:1920074/1‑71 (MQ=255)
                     ggTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAg                                        >  1:3789864/1‑71 (MQ=255)
                     ggTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAg                                        >  1:1796425/1‑71 (MQ=255)
                     ggTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAg                                        >  1:3735566/1‑71 (MQ=255)
                     ggTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAg                                        >  1:596779/1‑71 (MQ=255)
                         aaCAAGTATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCaa                                     >  1:1823443/1‑70 (MQ=255)
                         aaCAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTAt                                                                     >  1:824885/1‑38 (MQ=255)
                         aaCAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCaa                                     >  1:3655585/1‑70 (MQ=255)
                         aaCAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCaa                                     >  1:868902/1‑70 (MQ=255)
                         aaCAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCaa                                     >  1:1459473/1‑70 (MQ=255)
                                       gtCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCaaa                                    >  1:1899057/1‑57 (MQ=255)
                                       gtCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGt                       >  1:1710468/1‑70 (MQ=255)
                                       gtCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGt                       >  1:2567365/1‑70 (MQ=255)
                                       gtCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGt                       >  1:3405585/1‑70 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:578799/47‑1 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:849654/47‑1 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:1006235/47‑1 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:10304/47‑1 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:1590033/47‑1 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:3061012/47‑1 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:2362255/47‑1 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGa                                             <  1:3131232/47‑1 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAAGGTGGCATCGGTc                      >  1:3741630/1‑70 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGt                       >  1:3436249/1‑69 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTc                      >  1:3723425/1‑70 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTc                      >  1:965022/1‑70 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTc                      >  1:1005954/1‑70 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTc                      >  1:3909393/1‑70 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTc                      >  1:1834440/1‑70 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTc                      >  1:1937912/1‑70 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTc                      >  1:2182031/1‑70 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTc                      >  1:2339089/1‑70 (MQ=255)
                                        tCACTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTc                      >  1:3271953/1‑70 (MQ=255)
                                          aCTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCaa                    <  1:3173691/70‑1 (MQ=255)
                                          aCTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCaa                    <  1:3085988/70‑1 (MQ=255)
                                          aCTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCaa                    <  1:1152624/70‑1 (MQ=255)
                                          aCTCTTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCaa                    <  1:187438/70‑1 (MQ=255)
                                             ctTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAattca                >  1:680014/1‑71 (MQ=255)
                                             ctTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAattca                >  1:1444220/1‑71 (MQ=255)
                                             ctTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAattca                >  1:553243/1‑71 (MQ=255)
                                             ctTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAattca                >  1:3992898/1‑71 (MQ=255)
                                             ctTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAattca                >  1:1758855/1‑71 (MQ=255)
                                             ctTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAattca                >  1:338173/1‑71 (MQ=255)
                                             ctTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAattca                >  1:3172132/1‑71 (MQ=255)
                                             ctTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAattca                >  1:2215117/1‑71 (MQ=255)
                                             ctTTAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAattc                 >  1:1477272/1‑70 (MQ=255)
                                             cattAGCTAGCCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAattc                 >  1:2325066/3‑70 (MQ=255)
                                                  gctagcCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAAttcattca            <  1:3206287/70‑1 (MQ=255)
                                                  gctagcCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAAttcattca            <  1:1384024/70‑1 (MQ=255)
                                                  gctagcCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAAttcattca            <  1:764897/70‑1 (MQ=255)
                                                  gctagcCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAAttcattca            <  1:3624296/70‑1 (MQ=255)
                                                  gctagcCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAAttcattca            <  1:3210031/70‑1 (MQ=255)
                                                  gctagcCTTGTATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAAttcattca            <  1:3516099/70‑1 (MQ=255)
                                                  gctagcCTTGTATCGCATTGAACAAAACTTGAACCGATTTAACAAAACGTGGCATCGGTCAAttcattca            <  1:890541/70‑1 (MQ=255)
                                                      gcCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTg        <  1:3032094/70‑1 (MQ=255)
                                                      gcCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTg        <  1:368327/70‑1 (MQ=255)
                                                      gcCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTg        <  1:3672920/70‑1 (MQ=255)
                                                            cATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTtat  <  1:3964389/70‑1 (MQ=255)
                                                            |                                                                     
TTATCAGCGAAAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTAT  >  W3110S.gb/1620650‑1620779

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A