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 2,467,055 A→C 47.3% T173T (ACA→ACC)  atpA → F1 sector of membrane‑bound ATP synthase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,467,0550AC47.3% ‑4.3 / 114.6 93T173T (ACA→ACC) atpAF1 sector of membrane‑bound ATP synthase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (32/17);  new base C (27/17);  total (59/34)
Fisher's exact test for biased strand distribution p-value = 8.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

GATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGT  >  minE/2467004‑2467115
                                                   |                                                            
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:691166/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:2967547/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:2832191/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:703990/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:1236753/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:3112738/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:907203/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:1852028/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:425750/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:2052824/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTaa                                                         >  1:1352352/1‑57 (MQ=255)
gATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTa                                                          >  1:1078213/1‑56 (MQ=255)
   cccAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCg                                                    <  1:354851/59‑1 (MQ=255)
   cccAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCg                                                    <  1:804998/59‑1 (MQ=255)
   cccAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCg                                                    <  1:338511/59‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGTATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:865781/68‑1 (MQ=39)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCTTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:3038587/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:3428734/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:2292986/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:369452/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:2566217/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:1799922/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:1915177/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:1157942/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:1696053/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:1026721/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:1552206/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:1336946/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:1382312/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:768265/68‑1 (MQ=255)
      aaTCGGTCGTGGTCAGCATGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:59579/68‑1 (MQ=255)
         cGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACt                                                >  1:752535/1‑57 (MQ=255)
         cGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACt                                                >  1:2026913/1‑57 (MQ=255)
         cGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACt                                                >  1:134008/1‑57 (MQ=255)
         cGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACt                                                >  1:3128259/1‑57 (MQ=255)
         cGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGc                                    <  1:1085715/69‑1 (MQ=255)
          ggTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGc                                    >  1:3169001/1‑68 (MQ=255)
            tCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCcat                                 <  1:2997064/69‑1 (MQ=255)
             cGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACCGGTAAAACCGCACTGGCTATCg                                        <  1:273605/61‑1 (MQ=255)
                      cGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       <  1:2082390/69‑1 (MQ=255)
                      cGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       <  1:281038/69‑1 (MQ=255)
                      cGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       <  1:967802/69‑1 (MQ=255)
                      cGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       <  1:1290919/69‑1 (MQ=255)
                      cGTGAACTGATCAGCGTTTACCGTCAGACAGTTAAAACCGCAATGGCTATCg                                        <  1:2900956/52‑1 (MQ=255)
                         gAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAgcgc                    <  1:2627002/69‑1 (MQ=255)
                         gAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAgcgc                    <  1:1841113/69‑1 (MQ=255)
                            ttGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGa                  <  1:1727776/68‑1 (MQ=255)
                              gATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAgcgc                    >  1:3413369/1‑64 (MQ=255)
                              gATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTc               >  1:2510538/1‑69 (MQ=255)
                              gATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTc               >  1:1448247/1‑69 (MQ=255)
                                       tGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCa       <  1:324389/68‑1 (MQ=255)
                                       tGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCa       <  1:2643076/68‑1 (MQ=255)
                                       tGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCa       <  1:2940025/68‑1 (MQ=255)
                                       tGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCa       <  1:1516367/68‑1 (MQ=255)
                                          ccGTCAGACCTGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:3010181/1‑49 (MQ=38)
                                          ccGTCAGACCGGTAAAACCTCACTGGCTATCGATGCCATCATCAACCAg                       >  1:997188/1‑49 (MQ=38)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCcatc                                >  1:3032879/1‑40 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCa                        >  1:2776086/1‑48 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:2585247/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:1608820/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:1526751/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:680075/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:1496576/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:577859/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:557723/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:388114/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:2204636/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:2226503/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:2362760/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:3388162/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:2587562/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:3241845/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:3229257/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:2589184/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:1332644/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:902091/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:127990/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:3087708/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:1273976/1‑49 (MQ=255)
                                          ccGTCAGACCGGTAAAACCGCACTGGCTATCGATGACATCATCAACCAg                       >  1:3409180/1‑49 (MQ=39)
                                          ccGTCAGACCGGTAAAACAGCACTGGCTATCGATGCCATCATCAACCAg                       >  1:204693/1‑49 (MQ=38)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATg   >  1:2982558/1‑68 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATg   >  1:1228250/1‑68 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGt  >  1:2306019/1‑69 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGt  >  1:1486967/1‑69 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGt  >  1:1748434/1‑69 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGt  >  1:1781886/1‑69 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGt  >  1:3299817/1‑69 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGt  >  1:315755/1‑69 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGt  >  1:2699131/1‑69 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGt  >  1:2702760/1‑69 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGt  >  1:3072200/1‑69 (MQ=255)
                                           cGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGt  >  1:2816799/1‑69 (MQ=255)
                                                   |                                                            
GATCCCAATCGGTCGTGGTCAGCGTGAATTGATCATCGGTGACCGTCAGACAGGTAAAACCGCACTGGCTATCGATGCCATCATCAACCAGCGCGATTCCGGTATCAAATGT  >  minE/2467004‑2467115

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