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 2,253,207 G→A 43.2% G1277G (GGC→GGT)  rpoC ← RNA polymerase, beta prime subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,253,2070GA43.2% 30.7 / 73.1 97G1277G (GGC→GGT) rpoCRNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand):  ref base G (34/21);  new base A (23/19);  total (57/40)
Fisher's exact test for biased strand distribution p-value = 5.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

CCCACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGATAA  >  minE/2253142‑2253274
                                                                 |                                                                   
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCAcc                                                                   >  1:1661706/1‑68 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:2110956/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:3295480/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:101982/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:1698477/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:268040/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:361091/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:265646/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:2609436/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:504073/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:2429089/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:690623/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:850938/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCt                                                                  >  1:2327750/1‑69 (MQ=255)
cccACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCAGTTCACCt                                                                  >  1:78556/1‑69 (MQ=255)
              cGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGa                                                    >  1:979829/1‑69 (MQ=255)
              cGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGa                                                    >  1:2239652/1‑69 (MQ=255)
              cGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGa                                                    >  1:3317312/1‑69 (MQ=255)
              cGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGa                                                    >  1:1746809/1‑69 (MQ=255)
              cGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGa                                                    >  1:495876/1‑69 (MQ=255)
                        tCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCcgc                                           >  1:2374537/1‑68 (MQ=255)
                         cgcgGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCcgcg                                          >  1:1688756/1‑68 (MQ=255)
                         cgcgGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCcgcg                                          >  1:488905/1‑68 (MQ=255)
                         cgcgGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCcgcg                                          >  1:1407522/1‑68 (MQ=255)
                         cgcgGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCcgcg                                          >  1:1153714/1‑68 (MQ=255)
                         cgcgGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCcgcg                                          >  1:560290/1‑68 (MQ=255)
                         cgcgGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCcgcg                                          >  1:2334326/1‑68 (MQ=255)
                         cgcgGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCATTCCAGGAAGTCGGAGCTACCcgcg                                          >  1:2434128/1‑68 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGTTACCCGCGTTAACGAt                                  <  1:3386453/69‑1 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGTTACCCGCGTTAACGAt                                  <  1:2700901/69‑1 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGTTACCCGCGTTAACGAt                                  <  1:2516896/69‑1 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGTTACCCGCGTTAACGAt                                  <  1:2481607/69‑1 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGTTACCCGCGTTAACGAt                                  <  1:27303/69‑1 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGTTACCCGCGTTAACGAt                                  <  1:2334117/69‑1 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGAt                                  >  1:416136/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGAt                                  >  1:567980/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGAt                                  >  1:615595/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGAt                                  >  1:282217/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGAt                                  >  1:2647338/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGAt                                  >  1:2087608/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGAt                                  >  1:732212/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGAt                                  >  1:1650275/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGAt                                  >  1:505908/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGAt                                  >  1:3255269/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGAt                                  >  1:316636/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGAt                                  >  1:3054823/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGAt                                  >  1:2854605/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGAt                                  >  1:2243277/1‑69 (MQ=255)
                                tGCGATCTTGACGCGAGAGTATTCAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGAt                                  >  1:2255898/1‑69 (MQ=255)
                                 gCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTa                                                >  1:2460774/1‑54 (MQ=255)
                                   gATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATgg                                <  1:967596/68‑1 (MQ=255)
                                           cgcgAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAg                             <  1:1279703/63‑1 (MQ=255)
                                           cgcgAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAg                             <  1:975334/63‑1 (MQ=255)
                                           cgcgAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAg                             <  1:3379493/63‑1 (MQ=255)
                                           cgcgAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAg                             <  1:2134794/63‑1 (MQ=255)
                                                     ttCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTg             <  1:2965633/69‑1 (MQ=255)
                                                      tCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGATTTACGCAGCATCTg             <  1:2067597/68‑1 (MQ=255)
                                                       cAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCtt                          >  1:2951690/1‑54 (MQ=255)
                                                       cAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCtt                          >  1:2939850/1‑54 (MQ=255)
                                                       cAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCtt                          >  1:305125/1‑54 (MQ=255)
                                                       cAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCtt                          >  1:935932/1‑54 (MQ=255)
                                                       cAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCtt                          >  1:2850361/1‑54 (MQ=255)
                                                       cAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCtt                          >  1:693155/1‑54 (MQ=255)
                                                       cAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCtt                          >  1:2783725/1‑54 (MQ=255)
                                                       cAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGa            >  1:1093756/1‑68 (MQ=255)
                                                       cAACCTGTTCGCATTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCtt                          >  1:6863/1‑54 (MQ=255)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:1643327/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:1058222/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:1143887/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:97345/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:1112599/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:723022/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:2840394/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:2309609/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:2210829/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:2480463/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:2124489/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:2055187/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:296507/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:3017260/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:3262883/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:1864570/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:1873164/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:1929001/54‑1 (MQ=39)
                                                       cAACCTGTTCACCTTCCAGGAAGTCGGAGCTGCCCGCGTTAACGATGGTAGCtt                          <  1:3059920/54‑1 (MQ=39)
                                                           cTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGtt                                        >  1:2798553/1‑36 (MQ=255)
                                                           cTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGtt                                        >  1:3239455/1‑36 (MQ=255)
                                                             gTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGacgaacg      >  1:2015141/1‑68 (MQ=255)
                                                                cGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGAt    <  1:730777/67‑1 (MQ=255)
                                                                cGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGAt    <  1:3396499/67‑1 (MQ=255)
                                                                cGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGAt    <  1:1097485/67‑1 (MQ=255)
                                                                cGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGAt    <  1:2110764/67‑1 (MQ=255)
                                                                cGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGAt    <  1:2546757/67‑1 (MQ=255)
                                                                cGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGAt    <  1:942664/67‑1 (MQ=255)
                                                                cGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGAt    <  1:1376385/67‑1 (MQ=255)
                                                                cGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGAt    <  1:654822/67‑1 (MQ=255)
                                                                cGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGATaa  >  1:636537/1‑69 (MQ=255)
                                                                 |                                                                   
CCCACTTTGCCGTTCGCTTCCAGTTCGCGGTTTGCGATCTTGACGCGAGAGTATTCAACCTGTTCGCCTTCCAGGAAGTCGGAGCTACCCGCGTTAACGATGGTAGCTTTACGCAGCATCTGACGAACGATAA  >  minE/2253142‑2253274

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