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 535,717 T→C 57.2% L237L (CTA→CTG)  ybhG ← predicted membrane fusion protein (MFP) component of efflux pump, membrane anchor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE535,7170TC57.2% 30.1 / 67.4 92L237L (CTA→CTG) ybhGpredicted membrane fusion protein (MFP) component of efflux pump, membrane anchor
Reads supporting (aligned to +/- strand):  ref base T (18/21);  new base C (33/19);  total (51/41)
Fisher's exact test for biased strand distribution p-value = 1.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

Only 100 of 106 total aligned reads displayed.

TGGGCCTGGTCAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACA  >  minE/535661‑535784
                                                        |                                                                   
tGGGCCTGGTCAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTa                                                         <  1:2463081/69‑1 (MQ=255)
tGGGCCTGGTCAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTa                                                         <  1:843498/69‑1 (MQ=255)
   gCCTGGTCAAGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTaaat                                                      >  1:2239808/1‑68 (MQ=255)
   gCCTGGTCAAGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTaaat                                                      >  1:198382/1‑68 (MQ=255)
   gCCTGGTCAAGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTaaat                                                      >  1:2474782/1‑68 (MQ=255)
   gCCTGGTCAAGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTaaat                                                      >  1:1724251/1‑68 (MQ=255)
   gCCTGGTCAAGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTaaat                                                      >  1:3136818/1‑68 (MQ=255)
   gCCTGGTCAAGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTaaat                                                      >  1:1267392/1‑68 (MQ=255)
   gCCTGGTCAAGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTaaat                                                      >  1:513077/1‑68 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGt                                                 <  1:2956993/67‑1 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGt                                                 <  1:2300094/67‑1 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGt                                                 <  1:630874/67‑1 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGc                                               >  1:530653/1‑69 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGc                                               >  1:1034519/1‑69 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGc                                               >  1:1071921/1‑69 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGc                                               >  1:2425329/1‑69 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGc                                               >  1:723628/1‑69 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGc                                               >  1:2636352/1‑69 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGc                                               >  1:2778584/1‑69 (MQ=255)
          cAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGc                                               >  1:3221185/1‑69 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:2932359/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:2951092/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:253901/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:2716487/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:264134/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:3100645/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:2533685/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:252787/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:566907/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:772142/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:852619/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:2400584/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:396587/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:2297517/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:408536/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:2231231/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:1269810/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:1973743/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:1416148/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:2034671/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:1182726/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:1113860/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:1681030/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATAcc                                                   >  1:1094575/1‑64 (MQ=255)
           aaGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGt                                                 <  1:548247/66‑1 (MQ=255)
           aaGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGcc                                              >  1:2843223/1‑69 (MQ=255)
           aaGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGcc                                              >  1:2126175/1‑69 (MQ=255)
            aGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGcc                                              <  1:2859484/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:2686523/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:358855/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:563701/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:2615391/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:2576091/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:2563064/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:1216151/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:1946655/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:634425/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:670654/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:2369706/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:2137450/68‑1 (MQ=255)
             gATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:2254030/68‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:1714724/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:1218612/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:1193866/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:3427705/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:3334651/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:651253/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:1483582/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:290946/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:2810266/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:2349361/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:2074868/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:1984550/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:267141/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:1005699/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:2546187/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:1757921/69‑1 (MQ=255)
                    ttCATCAACATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:2621610/69‑1 (MQ=255)
                    ttCATCAAAATAGGCGCGTACCCACACCGGACGCGTCAGCGAGACGGTAAATACCGTGCCTCCTTCAtt                                     <  1:535001/69‑1 (MQ=255)
                                    cgcACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCa                                             <  1:2291881/45‑1 (MQ=255)
                                                   cgcgTTAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGtt      >  1:161531/1‑69 (MQ=255)
                                                   cgcgTTAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGtt      >  1:2368602/1‑69 (MQ=255)
                                                   cgcgTTAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGtt      >  1:546122/1‑69 (MQ=255)
                                                   cgcgTTAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGtt      >  1:3166157/1‑69 (MQ=255)
                                                   cgcgTTAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGtt      >  1:1272492/1‑69 (MQ=255)
                                                   cgcgTTAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGtt      >  1:124619/1‑69 (MQ=255)
                                                   cgcgTGAGCGAGACGGTAAATACCGTGCCACCTTCAtt                                     <  1:582851/38‑1 (MQ=21)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:1827962/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:928192/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:1098802/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:1725142/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:17409/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:1743391/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:363963/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:2572745/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:125022/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:431513/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:439556/1‑69 (MQ=255)
                                                       ttAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCCTTAACa  >  1:2525776/1‑69 (MQ=255)
                                                       ttAGAGAAACGATAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACa  >  1:3061476/1‑69 (MQ=255)
                                                        |                                                                   
TGGGCCTGGTCAAGATTACGTTCATCAACATAAGCGCGCACCCACACCGGACGCGTTAGTGAAACGGTAAACACCGTGCCACCTTCATTGAGGACCGTGCCTGGCTCCACCGCGCGCGTTAACA  >  minE/535661‑535784

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