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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,528,498 C→T 44.9% D83N (GAT→AAT)  dfp ← fused 4'‑phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase, FMN‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,528,4980CT44.9% 37.2 / 132.9 98D83N (GAT→AAT) dfpfused 4'‑phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase, FMN‑binding
Reads supporting (aligned to +/- strand):  ref base C (20/34);  new base T (35/9);  total (55/43)
Fisher's exact test for biased strand distribution p-value = 3.35e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.30e-02

ATTCGCCATTCCGGCAGCAACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCGGCTGCCGGGTCCAGCAGACTGTCGGAAAC  >  minE/2528433‑2528567
                                                                 |                                                                     
aTTCGCCATTCCGGCAGCAACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGcc                                                                   <  1:2794732/70‑1 (MQ=255)
   cGCCATTCCGGCAGCAACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               >  1:3328620/1‑71 (MQ=255)
    gCCATTCCGGCAGCAACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:3924682/70‑1 (MQ=255)
    gCCATTCCGGCAGCAACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:378085/70‑1 (MQ=255)
    gCCATTCCGGCAGCAACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:2688942/70‑1 (MQ=255)
    gCCATTCCGGCAGCAACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:3535160/70‑1 (MQ=255)
          ccGGCAGCAACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAg                                                        >  1:928/1‑71 (MQ=255)
          ccGGCAGCAACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAg                                                        >  1:3240737/1‑71 (MQ=255)
               agcaACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCaa                                                   <  1:4067947/71‑1 (MQ=255)
               agcaACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:2861028/71‑1 (MQ=255)
               agcaACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:2825924/71‑1 (MQ=255)
               agcaACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:380732/71‑1 (MQ=255)
               agcaACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:435589/71‑1 (MQ=255)
               agcaACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:1724254/71‑1 (MQ=255)
               agcaACACGGGCAATCAAATCTGCCGTAGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:3797350/71‑1 (MQ=255)
                   acacGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:2090864/55‑1 (MQ=255)
                    cacGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:3444058/66‑1 (MQ=255)
                    cacGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:1021432/66‑1 (MQ=255)
                      cGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTAccc                                                          >  1:1263640/1‑57 (MQ=255)
                      cGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAATATGGcc                                            >  1:315530/1‑71 (MQ=255)
                      cGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAATATGGc                                             >  1:12469/1‑70 (MQ=255)
                      cGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAata                                                 >  1:2852075/1‑66 (MQ=255)
                      cGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAata                                                 >  1:2619950/1‑66 (MQ=255)
                      cGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAATATGGcc                                            >  1:3906751/1‑71 (MQ=255)
                        ggCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:1299001/50‑1 (MQ=255)
                        ggCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAATATGGCCCa                                          >  1:3677813/1‑71 (MQ=255)
                         gCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:318030/61‑1 (MQ=255)
                            aTCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAATATGGcc                                            >  1:823897/1‑65 (MQ=255)
                             tCAAATCTTCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:2436616/45‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 <  1:3279501/43‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 <  1:2990245/43‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 <  1:1355259/43‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 <  1:1360183/43‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 <  1:2391534/43‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 <  1:1569837/43‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCa                                                                      <  1:3651737/38‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCa                                                                      <  1:1839352/38‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCa                                                                      <  1:357670/38‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCa                                                                      <  1:362679/38‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCa                                                                      <  1:3726472/38‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCa                                                                      <  1:1372105/38‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:2117195/45‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:1820900/45‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:1841823/45‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTAcc                                                           <  1:3905357/49‑1 (MQ=255)
                             tCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTAcc                                                           <  1:2918368/49‑1 (MQ=255)
                              cAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAATATGGCCCAt                                         >  1:2457009/1‑66 (MQ=255)
                              cAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAATATGGCCCAt                                         >  1:390955/1‑66 (MQ=255)
                              cAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAATATGGCCCATAg                                       >  1:1335488/1‑68 (MQ=255)
                              cAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAATATGGCCCATAg                                       >  1:2611291/1‑68 (MQ=255)
                              cAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAATATGGCCCATAGCgg                                    >  1:3685614/1‑71 (MQ=255)
                               aaaTCTGCCGTGGCTGGGGCGAGAATCACTAAATTAGCCCAtt                                                               >  1:945618/1‑43 (MQ=38)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCAtt                                                               >  1:3883889/1‑43 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCAtt                                                               >  1:4100343/1‑43 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCAtt                                                               >  1:1024186/1‑43 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCAtt                                                               >  1:1597611/1‑43 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCAtt                                                               >  1:2193793/1‑43 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCAtt                                                               >  1:2396512/1‑43 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAata                                                 >  1:1723867/1‑57 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAata                                                 >  1:911765/1‑57 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAata                                                 >  1:2327307/1‑57 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCATTTAACCAGCTCAATATgg                                              >  1:440720/1‑60 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAata                                                 >  1:2371231/1‑57 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGc                                   >  1:2021260/1‑71 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGc                                   >  1:887810/1‑71 (MQ=255)
                               aaaTCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGc                                   >  1:2466092/1‑71 (MQ=255)
                                 aTCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:3037775/53‑1 (MQ=255)
                                 aTCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:3535484/53‑1 (MQ=255)
                                  tCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 >  1:1281673/1‑38 (MQ=255)
                                  tCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 >  1:2425121/1‑38 (MQ=255)
                                  tCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 >  1:2994805/1‑38 (MQ=255)
                                  tCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 >  1:3527814/1‑38 (MQ=255)
                                  tCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 >  1:916367/1‑38 (MQ=255)
                                  tCTGCCGTGGCAGGGGCGAGAATCACTAAATTAGCCCa                                                                 >  1:3375976/1‑38 (MQ=255)
                                    tGCCGTGGCATGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCaa                                                   <  1:4116351/50‑1 (MQ=255)
                                    tGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCAtt                                                               <  1:3992509/38‑1 (MQ=255)
                                    tGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCa                                                         >  1:691870/1‑44 (MQ=255)
                                    tGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCa                                                         >  1:3035124/1‑44 (MQ=255)
                                    tGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCa                                                         >  1:3862530/1‑44 (MQ=255)
                                    tGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCa                                                         >  1:888776/1‑44 (MQ=255)
                                    tGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAata                                                 >  1:393667/1‑52 (MQ=255)
                                    tGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCgg                              >  1:2795580/1‑71 (MQ=255)
                                               gggCGAGAATCACTAAATTAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTc                                <  1:3264525/58‑1 (MQ=255)
                                                   gagaATCACTAAATTAGCCCATTTACCCAGCTCAata                                                 >  1:1382722/1‑37 (MQ=255)
                                                   gagaATCACTAAATTAGCCCATTTACCCAGCTCAata                                                 >  1:4071160/1‑37 (MQ=255)
                                                   gagaATCACTAAATTAGCCCATTTACCCAGCTCAata                                                 >  1:1729216/1‑37 (MQ=255)
                                                    agaATCACTAAATTAGCCCATTTACCCAGCTCAATATGGCCCATa                                        >  1:3303806/1‑45 (MQ=255)
                                                    agaATCACTAAATTAGCCCATTTACCCAGCTCAATATGGCCCATa                                        >  1:697982/1‑45 (MQ=255)
                                                    agaATCACTAAATTAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCGGCTGCCGGGTCcag                 >  1:2606615/1‑68 (MQ=255)
                                                      aaTCACTAAATCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCGGCTGCCGGGt                     >  1:2947871/1‑62 (MQ=255)
                                                          aCTAAATTAGCCCATTTACCCAGCTCAATATGGCCCATAGCgg                                    >  1:1220961/1‑43 (MQ=255)
                                                          aCTAAATTAGCCCATTTACCCAGCTCAATATGGCCCATAGCgg                                    >  1:3484386/1‑43 (MQ=255)
                                                              aaTTAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCGGCTGCCGGGTCCAGCAGACTGTCGGa     <  1:3442868/70‑1 (MQ=255)
                                                              aaTCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCGGCTGCCGGGTCCAGCAGACTGTCGGa     <  1:196401/70‑1 (MQ=255)
                                                               aTCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCGGCTGCCGGGTCcagcag              <  1:3081617/60‑1 (MQ=255)
                                                                tCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCGGCTGCCGGGTCCAGCAGACTGTCGGAAAc  >  1:2313158/1‑71 (MQ=255)
                                                                tCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCGGCTGCCGGGTCCAGCAGACTGTCGGAAAc  >  1:3302677/1‑71 (MQ=255)
                                                                tCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCGGCTGCCGGGTCCAGCAGACTGTCGGAAAc  >  1:3297954/1‑71 (MQ=255)
                                                                 |                                                                     
ATTCGCCATTCCGGCAGCAACACGGGCAATCAAATCTGCCGTGGCAGGGGCGAGAATCACTAAATCAGCCCATTTACCCAGCTCAATATGGCCCATAGCGGCTTCGGCTGCCGGGTCCAGCAGACTGTCGGAAAC  >  minE/2528433‑2528567

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