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 490,274 G→C 34.4% A218A (GCG→GCC)  pnuC → predicted nicotinamide mononucleotide transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE490,2740GC34.4% 119.4 / 96.6 122A218A (GCG→GCC) pnuCpredicted nicotinamide mononucleotide transporter
Reads supporting (aligned to +/- strand):  ref base G (47/33);  new base C (32/10);  total (79/43)
Fisher's exact test for biased strand distribution p-value = 7.27e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 123 total aligned reads displayed.

GTTATTTTTGCACTTCAGGGCGTTTACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTCACGCGCGCTGTCCCATT  >  minE/490209‑490338
                                                                 |                                                                
gtTATTTTTGCACTTCAGGGCGTTTACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTc                                                               <  1:1071464/69‑1 (MQ=255)
gtTATTTTTGCACTTCAGGGCGTTTACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTc                                                               <  1:2291055/69‑1 (MQ=255)
gtTATTTTTGCACTTCAGGGCGTTTACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTc                                                               <  1:2535789/69‑1 (MQ=255)
gtTATTTTTGCACTTCAGGGCGTTTACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTc                                                               <  1:1751052/69‑1 (MQ=255)
gtTATTTTTGCACTTCAGGGCGTTTACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTc                                                               <  1:3021570/69‑1 (MQ=255)
  tATTTTTGCACTTCAGGGCGTTTACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCaa                                                             >  1:2226321/1‑69 (MQ=255)
  tATTTTTGCACTTCAGGGCGTTTACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCaa                                                             >  1:333308/1‑69 (MQ=255)
                      tttACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTGGATCa                                         <  1:768461/69‑1 (MQ=255)
                      tttACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTGGATCa                                         <  1:1859333/69‑1 (MQ=255)
                      tttACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTGGATCa                                         <  1:694601/69‑1 (MQ=255)
                      tttACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTGGATCa                                         <  1:208614/69‑1 (MQ=255)
                      tttACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTGGATCa                                         <  1:2674035/69‑1 (MQ=255)
                      tttACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTGGATCa                                         <  1:2807008/69‑1 (MQ=255)
                      tttACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTGGATCa                                         <  1:473029/69‑1 (MQ=255)
                      tttACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTGGATCa                                         <  1:391977/69‑1 (MQ=255)
                      tttACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTGGATCa                                         <  1:773545/69‑1 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTTTTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:1647140/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGa                                                  <  1:1650253/58‑1 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGa                                                  <  1:2883742/58‑1 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGa                                                  <  1:822311/58‑1 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGa                                                  <  1:784550/58‑1 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGa                                                  <  1:2804352/58‑1 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGa                                                  <  1:1490199/58‑1 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGa                                                  <  1:2290317/58‑1 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGa                                                  <  1:2661153/58‑1 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCaa                                        >  1:1263322/1‑68 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:2372268/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:914185/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:787689/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:3081044/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:3280047/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:533059/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:646405/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:737217/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:73842/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:1160274/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:1180582/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:1242286/1‑69 (MQ=255)
                        tACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAAc                                       >  1:2198799/1‑69 (MQ=255)
                            ccATGTCTGTGGAGTACATCATCCTGACCTTTATTGCCCT‑AACgg                                                          >  1:2365711/1‑45 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:309370/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:1034196/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:909388/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:71183/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:1403342/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:1492771/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:503740/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:161604/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:3274379/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:1654302/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:2928128/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:2323593/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:2085090/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:2503928/1‑59 (MQ=255)
                            ccATGTCTCTGGAGTACATCATCCTGACCTATATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:1845955/1‑59 (MQ=255)
                            caaTGTCTCTGGAGTACATCATCCTGACCTTTATTGCCCTCAACGGCAGCCGGATGTgg                                             >  1:405576/3‑59 (MQ=255)
                                 tctcTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAgcg                                   >  1:2450295/1‑64 (MQ=255)
                                 tctcTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAgcg                                   >  1:1343660/1‑64 (MQ=255)
                                 tctcTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAgcg                                   >  1:203040/1‑64 (MQ=255)
                                 tctcTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAgcg                                   >  1:1462898/1‑64 (MQ=255)
                                 tctcTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAgcg                                   >  1:847486/1‑64 (MQ=255)
                                 tctcTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAgcg                                   >  1:2139174/1‑64 (MQ=255)
                                 tctcTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAgcg                                   >  1:1808636/1‑64 (MQ=255)
                                 tctcTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCAca                               >  1:2974184/1‑67 (MQ=255)
                                     tGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGa                            >  1:2418703/1‑67 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTgg                                             >  1:2377516/1‑43 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGa                            <  1:2951068/60‑1 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGa                            <  1:433920/60‑1 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGa                            <  1:3129913/60‑1 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGa                            <  1:2502289/60‑1 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGa                            <  1:127387/60‑1 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGa                            <  1:2994964/60‑1 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCt                    >  1:187914/1‑68 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCt                    >  1:3269722/1‑68 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTc                   >  1:659951/1‑69 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTc                   >  1:2697375/1‑69 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTc                   >  1:731642/1‑69 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTc                   >  1:1724790/1‑69 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTc                   >  1:1627542/1‑69 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTc                   >  1:1706344/1‑69 (MQ=255)
                                            catcatCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTc                   >  1:2524406/1‑69 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:1593483/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:2092952/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:490391/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:2432730/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:508670/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:239664/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:1115917/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:3203061/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:1342965/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:299573/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGCGAAAGAGGTTCAcg                >  1:2531981/1‑57 (MQ=255)
                                                           tATTGCCCTCAACGGCAGCCGGATGTGGAACAACAGCGCACGCGAAAGAGGTTCAc                 >  1:1668949/1‑56 (MQ=255)
                                                              tGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTCACGCGCGCTGTCCCAtt  <  1:2225329/68‑1 (MQ=255)
                                                              tGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTCACGCGCGCTGTCCCAtt  <  1:601314/68‑1 (MQ=255)
                                                              tGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTCACGCGCGCTGTCCCAtt  <  1:3298856/68‑1 (MQ=255)
                                                              tGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTCACGCGCGCTGTCCCAtt  <  1:3128319/68‑1 (MQ=255)
                                                              tGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTCACGCGCGCTGTCCCAtt  <  1:2643555/68‑1 (MQ=255)
                                                              tGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTCACGCGCGCTGTCCCAtt  <  1:1983408/68‑1 (MQ=255)
                                                               gcgcTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTCACGCGCGCTGTCCCAtt  <  1:1519918/67‑1 (MQ=255)
                                                                 |                                                                
GTTATTTTTGCACTTCAGGGCGTTTACGCCATGTCTCTGGAGTACATCATCCTGACCTTTATTGCGCTCAACGGCAGCCGGATGTGGATCAACAGCGCACGTGAAAGAGGCTCACGCGCGCTGTCCCATT  >  minE/490209‑490338

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