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 1,298,836 A→C 25.2% L80L (CTT→CTG)  cobU ← bifunctional cobinamide kinase and cobinamide phosphate guanylyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,298,8360AC25.2% 162.8 / 68.5 123L80L (CTT→CTG) cobUbifunctional cobinamide kinase and cobinamide phosphate guanylyltransferase
Reads supporting (aligned to +/- strand):  ref base A (49/43);  new base C (17/14);  total (66/57)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.76e-01

Only 100 of 123 total aligned reads displayed.

CATCAGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCAGCGCTCCA  >  minE/1298772‑1298903
                                                                |                                                                   
catcaGGGTCTTTATCGCCGCCATAATCAAACAACATATTAGTCACCATTGTGGTAACGCATTCAAGc                                                                  >  1:2036284/1‑68 (MQ=255)
catcaGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAg                                                                   >  1:1949750/1‑67 (MQ=255)
catcaGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGc                                                                  >  1:2057242/1‑68 (MQ=255)
catcaGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGc                                                                  >  1:2672100/1‑68 (MQ=255)
catcaGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGc                                                                  >  1:1722719/1‑68 (MQ=255)
catcaGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGc                                                                  >  1:357818/1‑68 (MQ=255)
catcaGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGc                                                                  >  1:2262018/1‑68 (MQ=255)
catcaGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGc                                                                  >  1:3289005/1‑68 (MQ=255)
    aGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAacac                                                             <  1:2867518/69‑1 (MQ=255)
    aGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAacac                                                             <  1:399848/69‑1 (MQ=255)
    aGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAacac                                                             <  1:367596/69‑1 (MQ=255)
    aGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAacac                                                             <  1:1231946/69‑1 (MQ=255)
    aGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAacac                                                             <  1:2482084/69‑1 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGTTAACGCATTCCAGCAAcacag                                                           <  1:2447476/69‑2 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:630240/69‑2 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:2954583/69‑2 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:1907312/69‑2 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:349011/69‑2 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:3053681/69‑2 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:3052248/69‑2 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:2752701/69‑2 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:1257970/69‑2 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:1266819/69‑2 (MQ=255)
      ggTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:932659/69‑2 (MQ=255)
       gTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCCAGCAAcacag                                                           <  1:2960985/68‑2 (MQ=255)
        tCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAAc                                                          >  1:1075639/1‑68 (MQ=255)
        tCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAAc                                                          >  1:3105278/1‑68 (MQ=255)
        tCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAAc                                                          >  1:963894/1‑68 (MQ=255)
                   gccATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              <  1:790429/69‑1 (MQ=255)
                    ccATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTa                                             <  1:1943061/69‑1 (MQ=255)
                    ccATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTa                                             <  1:779476/69‑1 (MQ=255)
                    ccATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTa                                             <  1:813995/69‑1 (MQ=255)
                      aTAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAAt                                           <  1:666112/69‑1 (MQ=255)
                      aTAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAAt                                           <  1:1198115/69‑1 (MQ=255)
                      aTAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAAt                                           <  1:921635/69‑1 (MQ=255)
                      aTAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAAt                                           <  1:1173698/69‑1 (MQ=255)
                      aTAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAAt                                           <  1:82197/69‑1 (MQ=255)
                      aTAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAAt                                           <  1:1475072/69‑1 (MQ=255)
                           cAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTg                                      <  1:2993931/69‑1 (MQ=255)
                           cAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTg                                      <  1:2990166/69‑1 (MQ=255)
                           cAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTg                                      <  1:3324911/69‑1 (MQ=255)
                           cAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTg                                      <  1:2704320/69‑1 (MQ=255)
                           cAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTg                                      <  1:764142/69‑1 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              <  1:940546/60‑1 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              >  1:2409121/1‑60 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              <  1:2816053/60‑1 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              <  1:1892942/60‑1 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              >  1:2312544/1‑60 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              <  1:2155713/60‑1 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              <  1:2137013/60‑1 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              <  1:487658/60‑1 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              <  1:1541870/60‑1 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              <  1:2029444/60‑1 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGtt                                              <  1:716609/60‑1 (MQ=255)
                            aaaCAACAGATTAGTCACCATTGAGGTAACGCATTCAAGCAACACAACCTCa                                                      >  1:2317940/1‑52 (MQ=255)
                              acaacaGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCa                                    <  1:2274614/68‑1 (MQ=255)
                              acaacaGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCa                                    <  1:2024163/68‑1 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:3027184/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:2962383/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:674156/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:979170/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:286634/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:258345/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:1507963/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:2874497/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:1143024/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:2282959/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaatta                             >  1:2279013/1‑67 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCCAGCAACACAGCCTCATTCGGGTTAATGTCTGCATGaataaa                            >  1:110629/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:1827907/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:1547598/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:1234263/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:3177613/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:2334588/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:2373796/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:2408231/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:2460219/1‑68 (MQ=255)
                                      ttAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:2500022/1‑68 (MQ=255)
                                      ttAGTCACAATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGaattaa                            >  1:2289914/1‑68 (MQ=255)
                                            aCCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATtca                        >  1:3173523/1‑66 (MQ=255)
                                            aCCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATtca                        >  1:2123372/1‑66 (MQ=255)
                                                ttGTGGTAACGGATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGAt                 <  1:74956/69‑1 (MQ=255)
                                                ttGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGAt                 <  1:2183887/69‑1 (MQ=255)
                                                ttGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGAt                 <  1:1392094/69‑1 (MQ=255)
                                                ttGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGAt                 <  1:3024018/69‑1 (MQ=255)
                                                 tgtgGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGa                  <  1:453669/67‑1 (MQ=255)
                                                    ggTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGtt              <  1:1707882/68‑1 (MQ=255)
                                                       aaCGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGcc           >  1:955119/1‑68 (MQ=255)
                                                       aaCGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCa          >  1:1842752/1‑69 (MQ=255)
                                                       aaCGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCa          >  1:590978/1‑69 (MQ=255)
                                                       aaCGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCa          >  1:143205/1‑69 (MQ=255)
                                                       aaCGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCa          >  1:1309982/1‑69 (MQ=255)
                                                       aaCGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCa          >  1:2133759/1‑69 (MQ=255)
                                                       aaCGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCa          >  1:1113287/1‑69 (MQ=255)
                                                       aaCGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCa          >  1:1093793/1‑69 (MQ=255)
                                                       aaCGAATTCAAGCAACACAACCTCATTCGGGTTaa                                            >  1:469367/1‑35 (MQ=255)
                                                               cAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCAGCGCTCCa  >  1:2084248/1‑69 (MQ=255)
                                                               cAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCAGCGCTCCa  >  1:3412544/1‑69 (MQ=255)
                                                               cAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCAGCGCTCCa  >  1:2789342/1‑69 (MQ=255)
                                                               cAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATAAAGATGtt              >  1:1940546/1‑57 (MQ=255)
                                                                |                                                                   
CATCAGGGTCTTTATCGCCGCCATAATCAAACAACAGATTAGTCACCATTGTGGTAACGCATTCAAGCAACACAACCTCATTCGGGTTAATGTCTGCATGAATTAATTCATCAAGATGTTGCCAGCGCTCCA  >  minE/1298772‑1298903

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