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 256,007 G→A 47.7% A84A (GCG→GCA)  yajC → SecYEG protein translocase auxillary subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE256,0070GA47.7% 15.6 / 114.0 132A84A (GCG→GCA) yajCSecYEG protein translocase auxillary subunit
Reads supporting (aligned to +/- strand):  ref base G (32/37);  new base A (51/12);  total (83/49)
Fisher's exact test for biased strand distribution p-value = 5.90e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 136 total aligned reads displayed.

GAACGGTGGCCTGGTTGGTCGCGTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCTGCCGAAAGGCACC  >  minE/255947‑256073
                                                            |                                                                  
gAACGGTGGCCTGGTTGGTCGCGTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAAt                                                              <  1:20323/67‑1 (MQ=255)
            ggttggtCGCGTAACCAAAGTAGCTGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAagt                                                <  1:1504089/69‑1 (MQ=255)
            ggttggtCGCGTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAagt                                                <  1:3150/69‑1 (MQ=255)
            ggttggtCGCGTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAagt                                                <  1:477976/69‑1 (MQ=255)
             gttggtCGCGTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAagta                                               >  1:3129369/1‑69 (MQ=255)
             gttggtCGCGTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAagta                                               >  1:3314253/1‑69 (MQ=255)
             gttggtCGCGTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAagta                                               >  1:3003346/1‑69 (MQ=255)
             gttggtCGCGTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAagta                                               >  1:2901482/1‑69 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGCCACCACTGAAGTAGttat                                          >  1:3367437/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGttat                                          >  1:2345862/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGttat                                          >  1:2142618/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGttat                                          >  1:2135954/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGttat                                          >  1:3428978/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGttat                                          >  1:168970/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGttat                                          >  1:893060/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGttat                                          >  1:1325861/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGttat                                          >  1:2517368/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGttat                                          >  1:1290178/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGttat                                          >  1:1205712/1‑68 (MQ=255)
                   cgcgTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGAACTGAATGACACCACTGAAGTAGttat                                          >  1:3296317/1‑68 (MQ=255)
                      gTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTaaa                                      >  1:2299033/1‑69 (MQ=255)
                      gTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTaaa                                      >  1:965200/1‑69 (MQ=255)
                      gTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTaaa                                      >  1:2555083/1‑69 (MQ=255)
                      gTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTaaa                                      >  1:2367894/1‑69 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:2890402/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:2333873/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:256401/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   >  1:3196165/1‑69 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   >  1:1837971/1‑69 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   >  1:410338/1‑69 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   >  1:1670783/1‑69 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:2867634/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:686274/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:1531252/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   >  1:580046/1‑69 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:1083971/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:2847413/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:3205410/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:3268787/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:413310/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:1524684/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:151862/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:1314226/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:824942/69‑1 (MQ=255)
                         aCCAAAGTAGCGGAAAACGGCTACATTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:856952/69‑1 (MQ=255)
                          ccAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGt                                   <  1:260387/68‑1 (MQ=255)
                                tAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCg                            <  1:731249/69‑1 (MQ=255)
                                tAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCg                            <  1:97996/69‑1 (MQ=255)
                                tAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCg                            <  1:2795047/69‑1 (MQ=255)
                                tAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCg                            <  1:1213976/69‑1 (MQ=255)
                                tAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCg                            <  1:1278827/69‑1 (MQ=255)
                                tAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCg                            <  1:1799608/69‑1 (MQ=255)
                                tAGCGGAAAACGCCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCg                            <  1:893632/69‑1 (MQ=255)
                                                 aTTGCTGTCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:2024/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGc                        >  1:2000153/1‑56 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:2212181/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:2713804/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:2039068/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:1932123/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:3354694/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:1818759/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:497807/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:538400/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:607827/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:1384112/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:1340260/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:869026/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:2483607/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:2796172/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:2776143/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:3096972/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:2652913/1‑57 (MQ=255)
                                                 aTTGCTATCGCACTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCt                       >  1:2461284/1‑57 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGATGTAGTTATTAAACGTGACTTCGTAGCTGCCGt                  >  1:314850/1‑58 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:1171402/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:2723733/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:1137060/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:2608093/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:2359240/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:2807406/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:1054800/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:2542357/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:1463425/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:2865181/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:2507242/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:1584646/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:430938/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:1600975/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:1768195/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:248342/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:2904785/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:2937898/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:330285/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:1982782/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               >  1:3242719/1‑61 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:3064710/61‑1 (MQ=255)
                                                     cTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCt               <  1:3188546/61‑1 (MQ=255)
                                                          gcgcTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCTGCCGAAAGGCAcc  >  1:685119/1‑69 (MQ=255)
                                                          gcgcTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCTGCCGAAAGGCAcc  >  1:832097/1‑69 (MQ=255)
                                                          gcgcTGAATGACACCACTGAAGTAGTTATTAAACGTCACTTCGTAGCTGCCGTCCTGCCGAAAGGCAcc  >  1:3109202/1‑69 (MQ=255)
                                                            |                                                                  
GAACGGTGGCCTGGTTGGTCGCGTAACCAAAGTAGCGGAAAACGGCTACATTGCTATCGCGCTGAATGACACCACTGAAGTAGTTATTAAACGTGACTTCGTAGCTGCCGTCCTGCCGAAAGGCACC  >  minE/255947‑256073

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