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 1,937,926 G→A 38.3% G55G (GGC→GGT)  dsbC ← protein disulfide isomerase II

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,937,9260GA38.3% 123.5 / 133.1 203G55G (GGC→GGT) dsbCprotein disulfide isomerase II
Reads supporting (aligned to +/- strand):  ref base G (98/27);  new base A (55/23);  total (153/50)
Fisher's exact test for biased strand distribution p-value = 2.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 204 total aligned reads displayed.

CCACTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATCGCTGCTTTTGATG  >  minE/1937864‑1937992
                                                              |                                                                  
ccACTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCt                                                               >  1:879763/1‑68 (MQ=255)
ccACTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCt                                                               >  1:1630747/1‑68 (MQ=255)
ccACTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCt                                                               >  1:1550102/1‑68 (MQ=255)
ccACTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCt                                                               >  1:1312779/1‑68 (MQ=255)
ccACTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCt                                                               >  1:1924116/1‑68 (MQ=255)
ccACTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCt                                                               >  1:280522/1‑68 (MQ=255)
ccACTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCt                                                               >  1:1753439/1‑68 (MQ=255)
ccACTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCt                                                               >  1:3143816/1‑68 (MQ=255)
  aCTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGtt                                                            <  1:1440099/69‑1 (MQ=255)
     aaCGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTa                                                           >  1:922977/1‑67 (MQ=255)
     aaCGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTa                                                           >  1:1256236/1‑67 (MQ=255)
     aaCGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTa                                                           >  1:2579936/1‑67 (MQ=255)
                 tGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCtt                                             <  1:1881312/69‑1 (MQ=255)
                 tGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCtt                                             <  1:3005543/69‑1 (MQ=255)
                 tGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCtt                                             <  1:1152062/69‑1 (MQ=255)
                  ggCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTc                                            >  1:285349/1‑69 (MQ=255)
                        tGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:2782108/1‑63 (MQ=255)
                        tGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:2163988/1‑63 (MQ=255)
                        tGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:2007290/1‑63 (MQ=255)
                        tGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:237343/1‑63 (MQ=255)
                        tGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:2838908/1‑63 (MQ=255)
                        tGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:2948350/1‑63 (MQ=255)
                        tGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:1474948/1‑63 (MQ=255)
                        tGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:395690/1‑63 (MQ=255)
                        tGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:48179/1‑63 (MQ=255)
                        tGAATGATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:1170457/1‑63 (MQ=255)
                            tGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTa                                  <  1:1962188/69‑1 (MQ=255)
                            tGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTa                                  <  1:2504824/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:3076350/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:3228517/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:2770595/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:2716805/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:1001552/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:434388/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:826212/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:267880/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:1803812/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:1712734/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:1906903/69‑1 (MQ=255)
                             gATATGTTTACCATCATCGGTGATGTACAACACACCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTAc                                 <  1:1666823/69‑1 (MQ=255)
                              atatGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACa                                >  1:3342483/1‑69 (MQ=255)
                              atatGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACa                                >  1:2265407/1‑69 (MQ=255)
                                atGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCtt                                             >  1:468184/1‑54 (MQ=255)
                                atGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCtt                                             >  1:3037409/1‑54 (MQ=255)
                                atGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAgg                              >  1:2245493/1‑69 (MQ=255)
                                atGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAgg                              >  1:2238585/1‑69 (MQ=255)
                                atGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAgg                              >  1:2447075/1‑69 (MQ=255)
                                atGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAgg                              >  1:3276627/1‑69 (MQ=255)
                                atGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAgg                              >  1:1458482/1‑69 (MQ=255)
                                atGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAgg                              >  1:2868823/1‑69 (MQ=255)
                                atGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAgg                              >  1:711941/1‑69 (MQ=255)
                                atGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAgg                              >  1:1843689/1‑69 (MQ=255)
                                 tGTTTACCATCATCGGTGATGTACAACACGCCGCTGt                                                             <  1:1592948/37‑1 (MQ=255)
                                 tGTTTACCATCATCGGTGATGTACAACACGCCGCTGt                                                             <  1:1512623/37‑1 (MQ=255)
                                 tGTTTACCATCATCGGTGATGTACAACACGCCGCTGt                                                             <  1:2992936/37‑1 (MQ=255)
                                 tGTTTACCATCATCGGTGATGTACAACACGCCGCTGt                                                             <  1:3302764/37‑1 (MQ=255)
                                   tttACCATCATCGGTGATGTACAACACGCCGCTGt                                                             >  1:1504515/1‑35 (MQ=255)
                                   tttACCATCATCGGTGATGTACAACACGCCGCTGt                                                             >  1:515212/1‑35 (MQ=255)
                                   tttACCATCATCGGTGATGTACAACACGCCGCTGt                                                             >  1:529140/1‑35 (MQ=255)
                                   tttACCATCATCGGTGATGTACAACACGCCGCTGt                                                             >  1:102303/1‑35 (MQ=255)
                                   tttACCATCATCGGTGATGTACAACACGCCGCTGt                                                             >  1:2126233/1‑35 (MQ=255)
                                   tttACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGgcgc                           >  1:708579/1‑69 (MQ=255)
                                   tttACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGgcgc                           >  1:2015737/1‑69 (MQ=255)
                                   tttACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGgcg                            >  1:3071719/1‑68 (MQ=255)
                                           catcGGTTATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGaa                   <  1:2527687/69‑1 (MQ=255)
                                           catcGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGaa                   <  1:658505/69‑1 (MQ=255)
                                           catcGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGaa                   <  1:593871/69‑1 (MQ=255)
                                           catcGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGaa                   <  1:3403129/69‑1 (MQ=255)
                                           catcGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGaa                   <  1:3312684/69‑1 (MQ=255)
                                            atcGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGaa                   >  1:654415/1‑68 (MQ=255)
                                            atcGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAat                  >  1:1284182/1‑69 (MQ=255)
                                            atcGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAat                  >  1:309821/1‑69 (MQ=255)
                                            atcGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAat                  >  1:3193190/1‑69 (MQ=255)
                                              cGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGTGCTGAatat                >  1:1676500/1‑69 (MQ=255)
                                              cGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAatat                >  1:2219875/1‑69 (MQ=255)
                                              cGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAatat                >  1:538151/1‑69 (MQ=255)
                                              cGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAatat                >  1:136307/1‑69 (MQ=255)
                                              cGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAatat                >  1:3199589/1‑69 (MQ=255)
                                              cGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAatat                >  1:1835538/1‑69 (MQ=255)
                                              cGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAatat                >  1:2875013/1‑69 (MQ=255)
                                               ggTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAatat                >  1:1344053/1‑68 (MQ=255)
                                               ggTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAata                 >  1:1209222/1‑67 (MQ=255)
                                               ggTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATc               >  1:3236164/1‑69 (MQ=255)
                                               ggTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATc               >  1:1391619/1‑69 (MQ=255)
                                               ggTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATc               >  1:1058312/1‑69 (MQ=255)
                                                  gATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:637845/1‑37 (MQ=255)
                                                  gATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:682359/1‑37 (MQ=255)
                                                  gATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:2376489/1‑37 (MQ=255)
                                                  gATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:801267/1‑37 (MQ=255)
                                                  gATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:2924091/1‑37 (MQ=255)
                                                  gATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:193823/1‑37 (MQ=255)
                                                  gATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:2711239/1‑37 (MQ=255)
                                                  gATGTACAACACACCGCTGTTAGTCAGAACTGTCTTc                                            >  1:2154958/1‑37 (MQ=255)
                                                        caacaCGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATCGCTGCtttt      >  1:366543/1‑69 (MQ=255)
                                                        caacaCGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATCGCTGCtttt      >  1:2033999/1‑69 (MQ=255)
                                                        caacaCGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATCGCTGCtttt      >  1:413445/1‑69 (MQ=255)
                                                        caacaCGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATCGCTGCtttt      >  1:240511/1‑69 (MQ=255)
                                                        caacaCGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATCGCTGCtttt      >  1:3202689/1‑69 (MQ=255)
                                                        caacaCGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATCGCTGCtttt      >  1:2958302/1‑69 (MQ=255)
                                                        caacaCGCCGCTGTTAGTCAGAACTGTCTTCACGCCAGCTACAGGCGCGGGCTGAATATCGCTGCtttt      >  1:2226472/1‑69 (MQ=255)
                                                              |                                                                  
CCACTAACGTCATACATTGGCCCCTGAATGATATGTTTACCATCATCGGTGATGTACAACACGCCGCTGTTAGTCAGAACTGTCTTCATGCCAGCTACAGGCGCGGGCTGAATATCGCTGCTTTTGATG  >  minE/1937864‑1937992

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