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 1,680,469 T→C 37.5% N1502S (AAC→AGC)  yfhM ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,680,4690TC37.5% 66.8 / 78.0 120N1502S (AAC→AGC) yfhMconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (39/36);  new base C (8/37);  total (47/73)
Fisher's exact test for biased strand distribution p-value = 2.16e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.72e-01

Only 100 of 120 total aligned reads displayed.

AACGAGTCCAGCGATTTGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATACGCAACCATAACGGCTGATC  >  minE/1680403‑1680533
                                                                  |                                                                
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:2354138/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:1606064/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:3168181/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:1475999/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:3006385/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:2977438/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:431392/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:2041503/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:2634297/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:630421/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:2191917/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:761137/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:1168551/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:2299635/69‑1 (MQ=255)
aaCGAGTCCAGCGATTTGCTCTTACCGTCAGTACCCAGAATATGACGCTCAATTTGCACCACATTGCTc                                                                <  1:2069956/69‑1 (MQ=255)
      tCCAGCGATTTGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTc                                                                >  1:1783113/1‑63 (MQ=255)
      tCCAGCGATTTGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCgg                                                           >  1:193906/1‑68 (MQ=255)
      tCCAGCGATTTGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCgg                                                           >  1:2632810/1‑68 (MQ=255)
      tCCAGCGATTTGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCgg                                                           >  1:3340585/1‑68 (MQ=255)
        cAGCGATTTGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTaa                                                        <  1:2477789/69‑1 (MQ=255)
               ttGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcg                                                 <  1:3254433/69‑1 (MQ=255)
               ttGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcg                                                 <  1:2801221/69‑1 (MQ=255)
               ttGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcg                                                 <  1:266390/69‑1 (MQ=255)
               ttGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcg                                                 <  1:1305825/69‑1 (MQ=255)
               ttGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcg                                                 <  1:1119687/69‑1 (MQ=255)
               ttGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcg                                                 <  1:2978992/69‑1 (MQ=255)
               ttGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcg                                                 <  1:1417996/69‑1 (MQ=255)
               ttGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcg                                                 <  1:2419497/69‑1 (MQ=255)
               ttGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcg                                                 <  1:1493398/69‑1 (MQ=255)
                tGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcg                                                 <  1:1487190/68‑1 (MQ=255)
                      tACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTCGCCGGTAAAgg                                                     >  1:786730/1‑58 (MQ=255)
                      tACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGtgcggattgcg                                          >  1:2401994/1‑69 (MQ=255)
                      tACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGtgcggattgcg                                          >  1:2580015/1‑69 (MQ=255)
                      tACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGtgcggattgcg                                          >  1:861807/1‑69 (MQ=255)
                      tACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGtgcggattgcg                                          >  1:541742/1‑69 (MQ=255)
                      tACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGtgcggattgcg                                          >  1:518988/1‑69 (MQ=255)
                      tACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGtgcggattgcg                                          >  1:2021227/1‑69 (MQ=255)
                      tACCGTCAGTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGtgcggattgcg                                          >  1:3134919/1‑69 (MQ=255)
                       aCCATCAGTACCAATAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAgg                                                     <  1:3285114/57‑1 (MQ=255)
                       aCCATCAGTACCAAGAATATGCCGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcggattgcg                                          >  1:1790379/1‑68 (MQ=255)
                       aCCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGc                                                              >  1:2876206/1‑48 (MQ=255)
                       aCCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcggattgcg                                          >  1:478502/1‑68 (MQ=255)
                       aCCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcggattgcg                                          >  1:2842619/1‑68 (MQ=255)
                       aCCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcggattgcg                                          >  1:2628371/1‑68 (MQ=255)
                       aCCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGtgcggattgcg                                          >  1:3429185/1‑68 (MQ=255)
                       aCCATCAGTACCAAGAAAATGACGCTCGATTTGCAGCACATAGTTCGCCGGTAAAGGtgcggattgcg                                          >  1:1343807/1‑68 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATaa                                     >  1:1219209/1‑68 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:2814725/1‑69 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:2517755/1‑69 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:299739/1‑69 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:1002770/1‑69 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:2377492/1‑69 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:2467901/1‑69 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:1722404/1‑69 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:174454/1‑69 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:1392279/1‑69 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:194149/1‑69 (MQ=255)
                            cAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAc                                    >  1:2373438/1‑69 (MQ=255)
                             aGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAgg                                                     >  1:1233534/1‑51 (MQ=255)
                             aGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAAcc                                   >  1:2956466/1‑69 (MQ=255)
                              gTACCCAGAATATGACGCTCAATTTGCAGCACATTGCTc                                                                <  1:2071604/39‑1 (MQ=37)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:321050/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:1582317/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:3150730/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:933476/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:3353364/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:1869846/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:1905501/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:1909310/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:69363/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:625569/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:2047792/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:1284607/69‑1 (MQ=255)
                                   aaGAATATGACGCTCGATTTGCAGCACATTGTCCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGc                             <  1:1574756/69‑1 (MQ=255)
                                      aaTATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATc                          >  1:928416/1‑69 (MQ=255)
                                      aaTATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATc                          >  1:657406/1‑69 (MQ=255)
                                      aaTATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATc                          >  1:2134629/1‑69 (MQ=255)
                                        tatGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATa                                      >  1:3364948/1‑55 (MQ=255)
                                          tGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATa                      >  1:81239/1‑69 (MQ=255)
                                          tGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATa                      >  1:123617/1‑69 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:764521/69‑1 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:112294/69‑1 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:2627033/69‑1 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:1642610/69‑1 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:822842/69‑1 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:221984/69‑1 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:2204418/69‑1 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:1281737/69‑1 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:1001343/69‑1 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:2523968/69‑1 (MQ=255)
                                              gCTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:942816/69‑1 (MQ=255)
                                               cTCAATTTGCAGCACATTGCTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCACACGCa                  <  1:3385836/68‑1 (MQ=255)
                                                           cacaTTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATACGCAACCATAACGGCTg     <  1:656060/69‑1 (MQ=255)
                                                           cacaTTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATACGCAACCATAACGGCTg     <  1:722382/69‑1 (MQ=255)
                                                           cacaTTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATACGCAACCATAACGGCTg     <  1:1230269/69‑1 (MQ=255)
                                                           cacaTTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATACGCAACCATAACGGCTg     <  1:282009/69‑1 (MQ=255)
                                                           cacaTTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATACGCAACCATAACGGCTg     <  1:1738078/69‑1 (MQ=255)
                                                               ttGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATACGCAACCATAACGGCTGATc  >  1:1206220/1‑68 (MQ=255)
                                                               ttGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATACGCAACCATAACGGCTGATc  >  1:1531819/1‑68 (MQ=255)
                                                               ttGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATACGCAACCATAACGGCTGATc  >  1:1694983/1‑68 (MQ=255)
                                                                  |                                                                
AACGAGTCCAGCGATTTGCTCTTACCATCAGTACCAAGAATATGACGCTCGATTTGCAGCACATTGTTCGCCGGTAAAGGTGCGGATTGCGGATAACCGCTGGCATCCATACGCAACCATAACGGCTGATC  >  minE/1680403‑1680533

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