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 2,476,553 G→A 32.9% A186A (GCG→GCA)  pstC → phosphate transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,476,5530GA32.9% 81.5 / 50.3 97A186A (GCG→GCA) pstCphosphate transporter subunit
Reads supporting (aligned to +/- strand):  ref base G (42/23);  new base A (19/13);  total (61/36)
Fisher's exact test for biased strand distribution p-value = 6.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01

Only 100 of 106 total aligned reads displayed.

ATTTGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTGGC  >  minE/2476490‑2476619
                                                               |                                                                  
aTTTGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGt                                                               <  1:922566/69‑1 (MQ=255)
aTTTGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGt                                                               <  1:470586/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:3144114/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:2552796/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:2637149/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:545312/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:2336409/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:2298143/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:2765952/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:2848059/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:1905293/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:2943656/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:423067/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:192717/69‑1 (MQ=255)
 tttGGTATCGGTATCCTCGCGGCAGGCGTGATACTCGCCATCATGATTATTCCGTACATTGCAGCGGTa                                                              <  1:3023227/69‑1 (MQ=255)
          ggtatcCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGt                                                               <  1:2447242/59‑1 (MQ=255)
          ggtatcCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGt                                                               <  1:46152/59‑1 (MQ=255)
          ggtatcCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGt                                                               <  1:1481239/59‑1 (MQ=255)
           gtatcCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGt                                                               <  1:810893/58‑1 (MQ=255)
              tcCTCGCGTCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGt                                                               <  1:1807071/55‑1 (MQ=255)
              tcCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGt                                                               <  1:475424/55‑1 (MQ=255)
                cTCGCGTCAGGCGTGATCCTCGCCATCATGATTATTCTGTACATAGCGGCGGTAATGCGTGATGTGtt                                                >  1:3943/1‑68 (MQ=255)
                cTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGtt                                                >  1:2966117/1‑68 (MQ=255)
                cTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGtt                                                >  1:1119430/1‑68 (MQ=255)
                cTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGtt                                                >  1:1798921/1‑68 (MQ=255)
                cTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGtt                                                >  1:1782432/1‑68 (MQ=255)
                            gTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCg                                   >  1:71009/1‑69 (MQ=255)
                            gTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCg                                   >  1:151939/1‑69 (MQ=255)
                            gTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCg                                   >  1:308041/1‑69 (MQ=255)
                            gTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCg                                   >  1:1465283/1‑69 (MQ=255)
                            gTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCg                                   >  1:2186693/1‑69 (MQ=255)
                              gATCCTCGCCATCATGATTATTGCGTACATTGCGGCGGt                                                               <  1:2743586/39‑1 (MQ=255)
                               aTCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtg                                >  1:3402552/1‑69 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAAt                                                            >  1:857674/1‑40 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:2569033/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:83774/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:686650/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:765306/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:529986/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:775535/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:3003768/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:308276/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:984246/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:1851411/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:2469420/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:2373672/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:2350430/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:1810602/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:981655/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:1254171/1‑55 (MQ=255)
                                tCCTCGCCATCATGATTATTCCGTACATTGCAGCGGTAATGCGCGATGTATTCGa                                             >  1:2161345/1‑55 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgat                              <  1:1419628/59‑1 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgat                              <  1:1523727/59‑1 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgat                              <  1:2889615/59‑1 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgat                              <  1:85377/59‑1 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgat                              <  1:2416764/59‑1 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:767642/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:630688/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:1486008/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:951008/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:1590535/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:3414424/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:807133/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:2378515/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:27139/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:1847812/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:2070802/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:2956410/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:267696/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAagag                    >  1:1851480/1‑69 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAaga                     >  1:2165162/1‑68 (MQ=255)
                                           atGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACACCGGTGATGATGAAagag                    >  1:1004133/1‑69 (MQ=255)
                                              attattCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCg                 >  1:124747/1‑69 (MQ=255)
                                                 attCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGcc              <  1:890956/69‑1 (MQ=255)
                                                 attCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGcc              >  1:211023/1‑69 (MQ=255)
                                                 attCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGcc              >  1:484876/1‑69 (MQ=255)
                                                 attCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGcc              >  1:526798/1‑69 (MQ=255)
                                                 attCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGcc              <  1:1102769/69‑1 (MQ=255)
                                                       tACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACgg         <  1:737028/68‑1 (MQ=255)
                                                       tACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACgg         <  1:1672028/68‑1 (MQ=255)
                                                       tACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACgg         <  1:76610/68‑1 (MQ=255)
                                                         cATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgatgatga                         >  1:2257899/1‑50 (MQ=255)
                                                         cATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgatgatga                         >  1:57974/1‑50 (MQ=255)
                                                         cATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgatgatga                         >  1:1566672/1‑50 (MQ=255)
                                                         cATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgatgatga                         >  1:1619349/1‑50 (MQ=255)
                                                         cATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgatgatga                         >  1:3352345/1‑50 (MQ=255)
                                                         cATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgatgatga                         >  1:3018630/1‑50 (MQ=255)
                                                         cATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGtgatgatga                         >  1:1823958/1‑50 (MQ=255)
                                                         cATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTAt      >  1:2708266/1‑69 (MQ=255)
                                                         cATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTAt      >  1:1232612/1‑69 (MQ=255)
                                                         cATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTAt      >  1:1066113/1‑69 (MQ=255)
                                                             gcggcgGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTgg   >  1:3038200/1‑68 (MQ=255)
                                                             gcggcgGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTgg   >  1:2892796/1‑68 (MQ=255)
                                                             gcggcgGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTgg   >  1:2541834/1‑68 (MQ=255)
                                                             gcggcgGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTGGc  >  1:359835/1‑69 (MQ=255)
                                                             gcggcgGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTGGc  >  1:3316425/1‑69 (MQ=255)
                                                             gcggcgGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTGGc  >  1:2664529/1‑69 (MQ=255)
                                                             gcggcgGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTGGc  >  1:1983516/1‑69 (MQ=255)
                                                             gcggcgGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTGGc  >  1:1046891/1‑69 (MQ=255)
                                                             gcggcgGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTGGc  >  1:1008763/1‑69 (MQ=255)
                                                               |                                                                  
ATTTGGTATCGGTATCCTCGCGGCAGGCGTGATCCTCGCCATCATGATTATTCCGTACATTGCGGCGGTAATGCGTGATGTGTTCGAACAAACCCCGGTGATGATGAAAGAGTCGGCCTACGGTATTGGC  >  minE/2476490‑2476619

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