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 1,441,372 G→C 33.1% A111A (GCG→GCC)  rcsD → phosphotransfer intermediate protein in two‑component regulatory system with RcsBC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,441,3720GC33.1% 81.5 / 61.6 82A111A (GCG→GCC) rcsDphosphotransfer intermediate protein in two‑component regulatory system with RcsBC
Reads supporting (aligned to +/- strand):  ref base G (38/16);  new base C (20/7);  total (58/24)
Fisher's exact test for biased strand distribution p-value = 7.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

TTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATC  >  minE/1441307‑1441433
                                                                 |                                                             
ttACAAGAGACGCGCCTGAAACTGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCg                                                               >  1:913112/1‑66 (MQ=255)
ttACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGtt                                                             >  1:904539/1‑68 (MQ=255)
            cgcCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGctct                                                <  1:1109390/69‑1 (MQ=255)
            cgcCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGctct                                                <  1:3106397/69‑1 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:2746050/1‑68 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:749022/1‑68 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:1625459/1‑68 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:874236/1‑68 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:1468767/1‑68 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:2182283/1‑68 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:2956798/1‑68 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:725464/1‑68 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:2388316/1‑68 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:1182577/1‑68 (MQ=255)
                tGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCAc                                             >  1:3296525/1‑68 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTg                                                     >  1:1078582/1‑57 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGctct                                                >  1:3323290/1‑62 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGctc                                                 >  1:3105710/1‑61 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:459154/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:1049329/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:2848301/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:2540550/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:599467/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:662885/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:1200901/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:536072/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:1207148/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:2952901/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:2239618/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:1265389/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:404036/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:3080712/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:1649951/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCTGGAAAAACCACGCCGCAAAAAGGAAGCCTTAAACTTTGGCtctc                                               >  1:2459475/1‑63 (MQ=255)
                   aaCAGGATGTCTACTATCT‑GAAAAACCACGCCGCAAAACGGAAGCCTTAATCTTTGGCtctc                                               >  1:3134839/1‑62 (MQ=255)
                       ggATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTc                                     <  1:3287037/69‑1 (MQ=255)
                       ggATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTc                                     <  1:95848/69‑1 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGtt                                                             >  1:2976928/1‑36 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGtt                                                             >  1:1357166/1‑36 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGtt                                                             >  1:1562890/1‑36 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGtt                                                             >  1:1744192/1‑36 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGtt                                                             >  1:412405/1‑36 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGtt                                                             >  1:280099/1‑36 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGtt                                                             >  1:2202429/1‑36 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGtt                                                             >  1:2332670/1‑36 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGc                                >  1:735831/1‑65 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGc                                >  1:3260549/1‑65 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGc                                >  1:458787/1‑65 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGc                                >  1:1106996/1‑65 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGc                                >  1:228872/1‑65 (MQ=255)
                                ctaTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGc                                >  1:2703377/1‑65 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCTTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:3156836/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:106798/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:772725/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:737047/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:440697/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:2253488/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:2263915/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:1503137/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:1391378/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:2906499/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:2972483/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:2935254/67‑1 (MQ=255)
                                  aTCTGGAGAAACCACGCCGCAAAACCGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTga                            <  1:3014703/67‑1 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAATCGTTAATCttt                                                      >  1:995595/1‑39 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGct                                                  >  1:998559/1‑43 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGAt                         >  1:3368769/1‑68 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATg                        >  1:2937240/1‑69 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATg                        >  1:357118/1‑69 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATg                        >  1:2494702/1‑69 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATg                        >  1:3413822/1‑69 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATg                        >  1:1498959/1‑69 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATg                        >  1:3171023/1‑69 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATg                        >  1:18795/1‑69 (MQ=255)
                                    cTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATg                        >  1:1687345/1‑69 (MQ=255)
                                             ccACGCCGCAAAACGGAAGCCTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAACgg               <  1:600216/69‑1 (MQ=255)
                                             ccACGCCGCAAAACGGAAGCCTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAACgg               <  1:1616031/69‑1 (MQ=255)
                                             ccACGCCGCAAAACGGAAGCCTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAACgg               <  1:1735052/69‑1 (MQ=255)
                                             ccACGCCGCAAAACGGAAGCCTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAACgg               <  1:679827/69‑1 (MQ=255)
                                             ccACGCCGCAAAACGGAAGCCTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAACgg               <  1:3213316/69‑1 (MQ=255)
                                             ccACGCCGCAAAACGGAAGCCTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAACgg               <  1:3020191/69‑1 (MQ=255)
                                             ccACGCCGCAAAACGGAAGCCTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAACgg               <  1:3316027/69‑1 (MQ=255)
                                                          cGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATc  >  1:2437541/1‑69 (MQ=255)
                                                                 |                                                             
TTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATC  >  minE/1441307‑1441433

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