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 2,245,860 G→A 26.9% P94P (CCG→CCA)  rsd → stationary phase protein, binds sigma 70 RNA polymerase subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,245,8600GA26.9% 97.1 / 32.3 85P94P (CCG→CCA) rsdstationary phase protein, binds sigma 70 RNA polymerase subunit
Reads supporting (aligned to +/- strand):  ref base G (15/47);  new base A (2/21);  total (17/68)
Fisher's exact test for biased strand distribution p-value = 1.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

TTTATGAGCGCATTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGATTCCAGTCTGGAAACCGCCATCGAT  >  minE/2245793‑2245926
                                                                   |                                                                  
tttATGAGCGCATTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGc                                                                   >  1:1294454/1‑69 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:2910045/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:361885/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:2083009/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:1573162/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:354584/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:2147462/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:620046/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:2045084/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:137377/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:3331863/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:797853/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:2683674/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:844490/69‑1 (MQ=255)
           aTTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:2697854/69‑1 (MQ=255)
             tcttcATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCaa                                                      <  1:704327/69‑1 (MQ=255)
             tcttcATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCaa                                                      <  1:1276098/69‑1 (MQ=255)
              cttcATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCaa                                                      >  1:509588/1‑68 (MQ=255)
              cttcATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCaa                                                      >  1:1808073/1‑68 (MQ=255)
              cttcATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCaa                                                      >  1:3399408/1‑68 (MQ=255)
              cttcATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCaa                                                      >  1:339093/1‑68 (MQ=255)
              cttcATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAAt                                                     >  1:46943/1‑69 (MQ=255)
              cttcATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAAt                                                     >  1:1339961/1‑69 (MQ=255)
              cttcATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAAt                                                     >  1:1602353/1‑69 (MQ=255)
                tcATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATa                                                    <  1:1580552/68‑1 (MQ=255)
                 cATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:3044191/63‑1 (MQ=255)
                 cATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:1621917/63‑1 (MQ=255)
                 cATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:991781/63‑1 (MQ=255)
                 cATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:3416412/63‑1 (MQ=255)
                 cATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGcc                                                        <  1:1518470/63‑1 (MQ=255)
                   tAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTc                                                 <  1:1097499/68‑1 (MQ=255)
                         ggAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGAt                                          <  1:1516066/69‑1 (MQ=255)
                         ggAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGAt                                          <  1:701868/69‑1 (MQ=255)
                         ggAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGAt                                          <  1:3378286/69‑1 (MQ=255)
                         ggAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGAt                                          <  1:1977255/69‑1 (MQ=255)
                         ggAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGAt                                          <  1:2863413/69‑1 (MQ=255)
                          gAAGGCAATGGGCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGAtt                                         >  1:537171/1‑69 (MQ=255)
                          gAAGGCAATGGGCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGAtt                                         >  1:528807/1‑69 (MQ=255)
                              gCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATgg                                     <  1:697308/69‑1 (MQ=255)
                              gCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATgg                                     <  1:235670/69‑1 (MQ=255)
                              gCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATgg                                     <  1:3131080/69‑1 (MQ=255)
                                aaCGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGAt                                   <  1:393837/69‑1 (MQ=255)
                                aaCGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGAt                                   <  1:820154/69‑1 (MQ=255)
                                aaCGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGAt                                   <  1:1141875/69‑1 (MQ=255)
                                aaCGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGAt                                   <  1:1310593/69‑1 (MQ=255)
                                aaCGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGAt                                   <  1:184982/69‑1 (MQ=255)
                                aaCGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGAt                                   <  1:2509017/69‑1 (MQ=255)
                                aaCGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGAt                                   <  1:2616083/69‑1 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCAGAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:2091981/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:1200587/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:862495/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:1365849/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:1369644/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:142217/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:465063/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:434454/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:3377638/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:3366378/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:3166607/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:2863901/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:2698795/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:2901707/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:3054285/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:2877851/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:3292507/67‑2 (MQ=255)
                                 atgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:3313260/67‑2 (MQ=255)
                                  tgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:3349475/67‑2 (MQ=255)
                                  tgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:2493562/67‑2 (MQ=255)
                                  tgggCAACTCGCACGCGCCGCGAAGATTTGGCCACAACTCGAAGCCAATACTCAACAGATTATGGAtg                                  <  1:698077/67‑2 (MQ=255)
                                      cAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGATtactac                             >  1:2046904/1‑69 (MQ=255)
                                      cAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGATtactac                             >  1:1663154/1‑69 (MQ=255)
                                         cTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGAt                          <  1:1420674/69‑1 (MQ=255)
                                         cTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGAt                          <  1:3329908/69‑1 (MQ=255)
                                           cgcgcgcgCCGCGAAGATTTGGCCGCAACTCGAAGCCaa                                                      <  1:355347/39‑1 (MQ=255)
                                           cgcgcgcgCCGCGAAGATTTGGCCGCAACTCGAAGCCaa                                                      >  1:3405597/1‑39 (MQ=255)
                                           cgcgcgcgCCGCGAAGATTTGGCCGCAACTCGAAGCCaa                                                      >  1:268527/1‑39 (MQ=255)
                                           cgcgcgcgCCGCGAAGATTTGGCCGCAACTCGAAGCCaa                                                      >  1:2287510/1‑39 (MQ=255)
                                           cgcgcgcgCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGAt                          >  1:1253432/1‑67 (MQ=255)
                                           cgcgcgcgCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGAt                          >  1:2979544/1‑67 (MQ=255)
                                                                  ggCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGATTCCAGTCTGGAAACCGCCATCGAt  <  1:2864566/67‑1 (MQ=255)
                                                                  cGCAACTCGAAGCCTATACTCAACAGATTATGGATTACTACGATTCCAGTCTGGAAACCGCCATCGAt  <  1:2180774/68‑1 (MQ=255)
                                                                  cGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGATTCCAGTCTGGAAACCGCCATCGAt  <  1:1580766/68‑1 (MQ=255)
                                                                  cGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGATTCCAGTCTGGAAACCGCCATCGAt  <  1:1254776/68‑1 (MQ=255)
                                                                  cGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGATTCCAGTCTGGAAACCGCCATCGAt  <  1:1781155/68‑1 (MQ=255)
                                                                  cGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGATTCCAGTCTGGAAACCGCCATCGAt  <  1:201212/68‑1 (MQ=255)
                                                                  cGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGATTCCAGTCTGGAAACCGCCATCGAt  <  1:883362/68‑1 (MQ=255)
                                                                   |                                                                  
TTTATGAGCGCATTCTTCATAAGCTGGAAGGCAACGGGCAACTCGCGCGCGCCGCGAAGATTTGGCCGCAACTCGAAGCCAATACTCAACAGATTATGGATTACTACGATTCCAGTCTGGAAACCGCCATCGAT  >  minE/2245793‑2245926

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