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 2,585,609 G→A 70.3% R556R (CGC→CGT)  mdtF ← multidrug transporter, RpoS‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,585,6090GA70.3% 50.4 / 24.5 57R556R (CGC→CGT) mdtFmultidrug transporter, RpoS‑dependent
Reads supporting (aligned to +/- strand):  ref base G (5/12);  new base A (38/2);  total (43/14)
Fisher's exact test for biased strand distribution p-value = 6.40e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

GTAACTGCGCGGTGGTCATAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGACCGGTACAA  >  minE/2585548‑2585675
                                                             |                                                                  
gTAACTGCGCGGTGGTCATAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTGCGCAgg                                                              >  1:2087672/1‑68 (MQ=255)
gTAACTGCGCGGTGGTCATAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGa                                                             <  1:1163828/69‑1 (MQ=255)
gTAACTGCGCGGTGGTCATAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGa                                                             <  1:1580342/69‑1 (MQ=255)
              gtCATAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTGCGCAGGAACAGCACCGCCATc                                               >  1:2744222/1‑69 (MQ=255)
                 aTAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATccc                                             >  1:3309798/1‑68 (MQ=255)
                 aTAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATccc                                             >  1:2160372/1‑68 (MQ=255)
                 aTAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATCCCg                                            >  1:2570255/1‑69 (MQ=255)
                 aTAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATCCCg                                            >  1:98254/1‑69 (MQ=255)
                 aTAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATCCCg                                            >  1:326180/1‑69 (MQ=255)
                 aTAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATCCCg                                            >  1:2630476/1‑69 (MQ=255)
                 aTAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATCCCg                                            >  1:2498242/1‑69 (MQ=255)
                 aTAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATCCCg                                            >  1:2046614/1‑69 (MQ=255)
                 aTAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATCCCg                                            >  1:1332036/1‑69 (MQ=255)
                 aTAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATCCCg                                            >  1:1027114/1‑69 (MQ=255)
                 aTAAATACCCACTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTACGCAGGAACAGCACCGCCATCCCg                                            >  1:2369050/1‑69 (MQ=255)
                                    cttctGGTAAGAAAGAGGTCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAg                          <  1:2964322/68‑1 (MQ=255)
                                    cttctGGTAAGAAAGAGGTCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAg                          <  1:216251/68‑1 (MQ=255)
                                    cttctGGTAAGAAAGAGGTCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAg                          <  1:2406229/68‑1 (MQ=255)
                                     ttctGGTAAGAAAGAGGTCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAg                          <  1:2536337/67‑1 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATcagc                                >  1:3193975/1‑46 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2838993/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2787287/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2876581/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2983812/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:305491/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:3061925/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:3255138/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:1172131/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:3289219/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:1123516/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:3348535/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:631723/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:741655/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:977820/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:1958799/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:1992205/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:1955947/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2229052/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2312612/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2386030/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2407020/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:1705784/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:1005834/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2589343/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2718504/1‑69 (MQ=255)
                                                    ggTCGGCGTACGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2729061/1‑69 (MQ=255)
                                                     gTCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:2631266/1‑68 (MQ=255)
                                                     gTCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:813466/1‑68 (MQ=255)
                                                     gTCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGAcc         >  1:960808/1‑68 (MQ=255)
                                                      tCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGACCgg       <  1:1517685/69‑1 (MQ=255)
                                                      tCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGACCgg       <  1:615323/69‑1 (MQ=255)
                                                      tCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGACCgg       <  1:20693/69‑1 (MQ=255)
                                                      tCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACAACCATGTAGCGACCgg       <  1:3141093/69‑1 (MQ=255)
                                                      tCGGCGTGCGCAGGAACAGCACCG‑CATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGACCgg       <  1:2281180/68‑1 (MQ=255)
                                                           gTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGACCGGTACaa  <  1:180645/69‑1 (MQ=255)
                                                           gTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGACCGGTACaa  <  1:2060594/69‑1 (MQ=255)
                                                            tGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGACCGGTACaa  <  1:433800/68‑1 (MQ=255)
                                                             |                                                                  
GTAACTGCGCGGTGGTCATAAATACCCCCTGATCCTCTTCTGGTAAGAAAGAGGTCGGCGTGCGCAGGAACAGCACCGCCATCCCGGCGCAAATCAGCAGGTAGACCACCATGTAGCGACCGGTACAA  >  minE/2585548‑2585675

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