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 266,955 G→A 63.0% G564G (GGC→GGT)  dxs ← 1‑deoxyxylulose‑5‑phosphate synthase, thiamine‑requiring, FAD‑requiring

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE266,9550GA63.0% 55.7 / 63.3 100G564G (GGC→GGT) dxs1‑deoxyxylulose‑5‑phosphate synthase, thiamine‑requiring, FAD‑requiring
Reads supporting (aligned to +/- strand):  ref base G (30/7);  new base A (34/29);  total (64/36)
Fisher's exact test for biased strand distribution p-value = 9.16e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.19e-01

Only 100 of 114 total aligned reads displayed.

GTTCAGCACGGGTACTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCATGGCTGGCGGCCATTTCCAGAATT  >  minE/266895‑267021
                                                            |                                                                  
gTTCATCACGGGTACTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCAt                                                            <  1:3362027/69‑1 (MQ=255)
gTTCAGCACGGGTACTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCAt                                                            <  1:2340898/69‑1 (MQ=255)
gTTCAGCACGGGTACTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCAt                                                            <  1:2497282/69‑1 (MQ=255)
gTTCAGCACGGGTACTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCAt                                                            <  1:771623/69‑1 (MQ=255)
gTTCAGCACGGGTACTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCAt                                                            <  1:1389585/69‑1 (MQ=255)
   cAGAACGGGTACTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAAt                                                         >  1:2025259/1‑69 (MQ=255)
              cTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCgccgcc                                                               <  1:1000379/52‑1 (MQ=255)
              cTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCgccgcc                                                               <  1:2052980/52‑1 (MQ=255)
              cTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCgccgcc                                                               <  1:2673952/52‑1 (MQ=255)
              cTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCgccgcc                                                               <  1:1780028/52‑1 (MQ=255)
              cTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCgccgcc                                                               <  1:3226880/52‑1 (MQ=255)
              cTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCgccgcc                                                               <  1:370650/52‑1 (MQ=255)
               tGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCgccgcc                                                               <  1:1113280/51‑1 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:1468687/1‑69 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:963031/1‑69 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:2203569/1‑69 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:962911/1‑69 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:2584603/1‑69 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:2808743/1‑69 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:2862946/1‑69 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:2978183/1‑69 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:3015846/1‑69 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:1488895/1‑69 (MQ=255)
                 gTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTa                                           >  1:2983731/1‑69 (MQ=255)
                   ttACGATGGGGCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:2063880/50‑1 (MQ=38)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:256479/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:1058740/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:482988/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:2292776/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:519729/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:2405674/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:318651/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:2566078/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:3139899/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:560682/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:53032/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:3001002/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:2865188/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:2036503/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:1480751/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:1503324/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:1158514/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:1523232/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:1690073/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:1693165/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:1747556/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:1275837/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:1391416/50‑1 (MQ=39)
                   ttACGATGGGCCATCAGCACTTCGTACACGCCGCTGCCTGCACCACCCAt                                                            <  1:3201645/50‑1 (MQ=255)
                       gATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCgccgcc                                                               <  1:85874/43‑1 (MQ=255)
                         tGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:2145781/44‑1 (MQ=38)
                              cATCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCAt                                                            <  1:108849/39‑1 (MQ=37)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCTATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:1597235/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCTTTTTCTTCTACGGTAACCAgcgc                              >  1:3353804/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTAc                                          >  1:49406/1‑56 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:1863232/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:1991146/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:3420541/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:3232808/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:2357602/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:1978725/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:1533365/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:3072290/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:1549274/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:395687/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:1620899/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:677025/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:2839739/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:1976556/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:2749034/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:2614473/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:2587611/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCCGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:490496/1‑68 (MQ=255)
                               aTCAGCACTTCGTTCACGCAGCTGCCTGCACCACCCATAATGGCGTTTTCTTCTACGGTAACCAgcgc                              >  1:3094062/1‑68 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTttcttc                                             >  1:755114/1‑50 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTttcttc                                             >  1:1203341/1‑50 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTttcttc                                             >  1:380245/1‑50 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTttcttc                                             >  1:447640/1‑50 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTttcttc                                             >  1:786500/1‑50 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTttcttc                                             >  1:2132546/1‑50 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTttcttc                                             >  1:3104726/1‑50 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTttcttc                                             >  1:2797895/1‑50 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTttcttc                                             >  1:2137466/1‑50 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCa                          >  1:340864/1‑69 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCa                          >  1:1405856/1‑69 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCa                          >  1:1915066/1‑69 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCa                          >  1:1999947/1‑69 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCa                          >  1:1936755/1‑69 (MQ=255)
                                  aGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCa                          >  1:2409066/1‑69 (MQ=255)
                                        tCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTAc                                          >  1:2464670/1‑47 (MQ=255)
                                        tCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCAtggctg                    >  1:3313790/1‑69 (MQ=255)
                                        tCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCAtggctg                    >  1:1587015/1‑69 (MQ=255)
                                        tCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCAtggct                     >  1:1811424/1‑68 (MQ=255)
                                        tCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCAtggc                      >  1:1083126/1‑67 (MQ=255)
                                                       cctgcGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCATGGCTGGCGGCCATTTCCAGa     >  1:248587/1‑69 (MQ=255)
                                                       cctgcGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCATGGCTGGCGGCCATTTCCAGa     >  1:331915/1‑69 (MQ=255)
                                                       cctgcGACGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCATGGCTGGCGGCCATTTCCAGa     >  1:1979142/1‑69 (MQ=255)
                                                          gcgcCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCATGGCTGGCGGCCATTTCCAGAAtt  <  1:2295504/69‑1 (MQ=255)
                                                          gcgcCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCATGGCTGGCGGCCATTTCCAGAAtt  <  1:138795/69‑1 (MQ=255)
                                                           cgccgcCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCATGGCTGGCGGCCATTTCCAGAAtt  <  1:2579598/68‑1 (MQ=255)
                                                            |                                                                  
GTTCAGCACGGGTACTGGTTTACGATGGGCCATCAGCACTTCGTTCACGCCGCTGCCTGCGCCGCCCATAATGGCGTTTTCTTCTACGGTGACCAGCGCTTCATGGCTGGCGGCCATTTCCAGAATT  >  minE/266895‑267021

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