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 2,694,016 A→G 31.7% R204R (CGT→CGC)  yrfF ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,694,0160AG31.7% 91.3 / 54.2 107R204R (CGT→CGC) yrfFpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (21/52);  new base G (21/13);  total (42/65)
Fisher's exact test for biased strand distribution p-value = 1.49e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 107 total aligned reads displayed.

ATCAGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAATATTGAGTAG  >  minE/2693966‑2694078
                                                  |                                                              
aTCAGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGgacga                                              >  1:660165/1‑69 (MQ=255)
aTCAGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGgacga                                              >  1:2559008/1‑69 (MQ=255)
aTCAGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGgacga                                              >  1:1973703/1‑69 (MQ=255)
  cAGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGgacga                                              >  1:52997/1‑67 (MQ=255)
  cAGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGgacga                                              >  1:2534608/1‑67 (MQ=255)
  cAGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGgacga                                              >  1:2403265/1‑67 (MQ=255)
  cAGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGgacga                                              >  1:1314783/1‑67 (MQ=255)
   aGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACTCTTCACGCAGCCcgcgcg                                                   <  1:27975/61‑1 (MQ=255)
   aGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   <  1:1035153/61‑1 (MQ=255)
   aGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   <  1:387143/61‑1 (MQ=255)
   aGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   <  1:3118501/61‑1 (MQ=255)
   aGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   <  1:3057419/61‑1 (MQ=255)
   aGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   <  1:276362/61‑1 (MQ=255)
   aGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   <  1:1862974/61‑1 (MQ=255)
   aGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   <  1:1650032/61‑1 (MQ=255)
   aGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   <  1:1612147/61‑1 (MQ=255)
   aGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   <  1:1308436/61‑1 (MQ=255)
    ggCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   <  1:1979183/60‑1 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGTTTCGCGCAGcc                                                         >  1:1481834/1‑53 (MQ=25)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:1161875/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:1083323/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:3205630/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:1202046/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:2650355/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:3357/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:3425896/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:128726/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:34456/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:2033048/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:414948/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:1690349/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:857628/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:1009341/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:1671446/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:1394026/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:1620087/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCCCGCGCGGACGACTCa                                          >  1:1618262/1‑68 (MQ=255)
     gCAGAAAAAGAACATCATGAAGGAGGCGACAATCAGCAACGCTTCGCGCAGCC‑‑CGCGGACGACTCa                                          >  1:1853676/1‑66 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCcgcgcg                                                   >  1:2401334/1‑54 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      <  1:591697/67‑1 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      <  1:3321119/67‑1 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      <  1:158573/67‑1 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      <  1:911753/67‑1 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      <  1:1455892/67‑1 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      <  1:2122794/67‑1 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      <  1:2081820/67‑1 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      >  1:1041394/1‑67 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      >  1:1861892/1‑67 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      <  1:580513/67‑1 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACACAgcgc                                      >  1:1229643/1‑67 (MQ=255)
          aaaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCCCGCGGACGACTCAgcgc                                      >  1:125764/1‑67 (MQ=255)
           aaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCata                                   <  1:3106029/69‑1 (MQ=255)
           aaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCata                                   <  1:414460/69‑1 (MQ=255)
           aaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCata                                   <  1:641952/69‑1 (MQ=255)
           aaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCata                                   <  1:3281675/69‑1 (MQ=255)
           aaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCat                                    >  1:1971318/1‑68 (MQ=255)
           aaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCat                                    >  1:1465581/1‑68 (MQ=255)
           aaaGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCat                                    >  1:3214084/1‑68 (MQ=255)
             aGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCa                                     >  1:233405/1‑65 (MQ=255)
                 cATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      <  1:2613961/60‑1 (MQ=255)
                 cATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATAttcttc                             <  1:1826613/69‑1 (MQ=255)
                 cATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATAttcttc                             <  1:2284711/69‑1 (MQ=255)
                 cATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATAttcttc                             <  1:1049053/69‑1 (MQ=255)
                  aTCAGGAAGGATGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATAttcttc                             <  1:1587112/68‑1 (MQ=255)
                  aTCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATAttcttc                             <  1:1464016/68‑1 (MQ=255)
                  aTCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATAttcttc                             <  1:1460208/68‑1 (MQ=255)
                  aTCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATAttcttc                             <  1:1196926/68‑1 (MQ=255)
                  aTCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATAttcttc                             <  1:2463232/68‑1 (MQ=255)
                       gaaggaGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGt                       <  1:148627/69‑1 (MQ=255)
                       gaaggaGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGt                       <  1:528723/69‑1 (MQ=255)
                       gaaggaGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGt                       <  1:2771063/69‑1 (MQ=255)
                         aggaggCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCATGCGt                       <  1:3343760/67‑1 (MQ=255)
                           gaggCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAgcgc                                      <  1:2926260/50‑1 (MQ=255)
                                  cgaTCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGaa            <  1:573314/69‑1 (MQ=255)
                                  cgaTCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGaa            <  1:3299889/69‑1 (MQ=255)
                                      cAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAata          <  1:3052230/67‑1 (MQ=255)
                                      cAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAata          <  1:991116/67‑1 (MQ=255)
                                      cAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAata          >  1:878380/1‑67 (MQ=255)
                                      cAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAata          <  1:2086563/67‑1 (MQ=255)
                                      cAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAata          <  1:2950263/67‑1 (MQ=255)
                                      cAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAata          >  1:3208572/1‑67 (MQ=255)
                                      cAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAata          <  1:2899679/67‑1 (MQ=255)
                                      cAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAata          >  1:319895/1‑67 (MQ=255)
                                      cAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAat           >  1:1542788/1‑66 (MQ=255)
                                       aGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAata          <  1:1357345/66‑1 (MQ=255)
                                       aGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAata          <  1:1571878/66‑1 (MQ=255)
                                         cAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGt                       <  1:253608/51‑1 (MQ=255)
                                            cGCTTCGCGCAGCCCGCGCTGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:1852909/69‑1 (MQ=37)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:3007973/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:950835/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:811863/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:646340/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:1673450/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:2857355/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:3208384/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:1900799/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:2024396/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:2284058/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:2419136/69‑1 (MQ=38)
                                            cGCTTCGCGCAGCCCGCGCGGACGACTCAGCGCATACTCTTCGTGCGTTTCTTTGCGAATATTGAGCAg  <  1:3379077/69‑1 (MQ=38)
                                                  |                                                              
ATCAGGCAGAAAAAGAACATCAGGAAGGAGGCGACGATCAGCAACGCTTCACGCAGCCCGCGCGGACGACTCAGCGCATATTCTTCATGCGTTTCTTTGCGAATATTGAGTAG  >  minE/2693966‑2694078

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A