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 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,496,561 C→T 41.8% M327I (ATG→ATA)  nuoF ← NADH:ubiquinone oxidoreductase, chain F

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,496,5610CT41.8% 40.1 / 82.0 67M327I (ATG→ATA) nuoFNADH:ubiquinone oxidoreductase, chain F
Reads supporting (aligned to +/- strand):  ref base C (24/15);  new base T (20/8);  total (44/23)
Fisher's exact test for biased strand distribution p-value = 4.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.64e-01

TCACGGGCGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCAAG  >  minE/1496496‑1496629
                                                                 |                                                                    
tCACGGGCGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCCa                                                                     >  1:3272950/1‑67 (MQ=255)
  aCGGGCGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGc                                                                 >  1:839877/1‑69 (MQ=255)
     ggCGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAgcg                                                            >  1:2566231/1‑71 (MQ=255)
     ggCGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAgcg                                                            >  1:583042/1‑71 (MQ=255)
     ggCGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAgcg                                                            >  1:144235/1‑71 (MQ=255)
      gCGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAgcgc                                                           <  1:2810321/71‑1 (MQ=255)
      gCGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAgcgc                                                           <  1:1086466/71‑1 (MQ=255)
      gCGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAgcgc                                                           <  1:1934860/71‑1 (MQ=255)
       cGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCCATCGCCAGCGcc                                                          >  1:1009145/1‑71 (MQ=255)
                    cAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTAGCCAGACGGc                                             >  1:1884556/1‑71 (MQ=255)
                    cAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGa                                                 >  1:4089282/1‑67 (MQ=255)
                    cAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGa                                                 >  1:3081245/1‑67 (MQ=255)
                    cAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGa                                                 >  1:2559360/1‑67 (MQ=255)
                    cAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGc                                             >  1:817202/1‑71 (MQ=255)
                    cAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGc                                             >  1:1920754/1‑71 (MQ=255)
                    cAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGc                                             >  1:2459413/1‑71 (MQ=255)
                        ttACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGcc                                         >  1:777725/1‑71 (MQ=255)
                         tACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGccc                                        >  1:2755393/1‑71 (MQ=255)
                         tACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCCa                                                                     >  1:655821/1‑42 (MQ=255)
                         tACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCCa                                                                     >  1:2400537/1‑42 (MQ=255)
                         tACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCCa                                                                     >  1:215613/1‑42 (MQ=255)
                         tACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAg                                                  >  1:2385683/1‑61 (MQ=255)
                         tACGCACCAGCGACACCACGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGa                                                 >  1:1942991/1‑62 (MQ=255)
                              aCCAGCGACACCATGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCttt                                   <  1:1110041/71‑1 (MQ=255)
                              aCCAGCGACACCATGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCttt                                   <  1:516208/71‑1 (MQ=255)
                               ccAGCGACACCATGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCa                                                   <  1:9535/54‑1 (MQ=255)
                               ccAGCGACACCATGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCa                                                   <  1:1000040/54‑1 (MQ=255)
                                  gCGACACCATGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTAcc                                >  1:2256956/1‑70 (MQ=255)
                                  gCGACACCATGTTGATCTCATGGTCAACC‑CTATCGCCAGCGCCGTACCCAGACGGCTGccctc                                      <  1:4251071/63‑3 (MQ=255)
                                   cGACACCATGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGa                              <  1:686100/71‑1 (MQ=255)
                                    gACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGAt                             <  1:35341/71‑1 (MQ=255)
                                    gACACCATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGAt                             <  1:1164334/71‑1 (MQ=255)
                                        ccATGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACtt                         <  1:3648880/71‑1 (MQ=255)
                                         cATGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACttt                        >  1:81879/1‑71 (MQ=255)
                                          aTGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTc                       >  1:2515142/1‑71 (MQ=255)
                                          aTGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTc                       >  1:686029/1‑71 (MQ=255)
                                          aTGTTGATCTCATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTc                       >  1:3627135/1‑71 (MQ=255)
                                          aTGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTc                       >  1:1086927/1‑71 (MQ=255)
                                          aTGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTc                       >  1:3210492/1‑71 (MQ=255)
                                          aTGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTc                       >  1:598654/1‑71 (MQ=255)
                                              tGATCTCATGGTCAACCGCCATCGCCAGCGCCGTa                                                       >  1:1917609/1‑35 (MQ=255)
                                              tGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGa                                                 >  1:498368/1‑41 (MQ=255)
                                              tGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGa                                                 >  1:4189002/1‑41 (MQ=255)
                                              tGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGa                                                 >  1:1619887/1‑41 (MQ=255)
                                                  ctcATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCa               >  1:2310305/1‑71 (MQ=255)
                                                  ctcATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCa               >  1:2308084/1‑71 (MQ=255)
                                                  ctcATGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCa               >  1:2046987/1‑71 (MQ=255)
                                                   tcATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGAt                             <  1:779680/56‑1 (MQ=255)
                                                     aTGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCAt              <  1:2000283/69‑1 (MQ=255)
                                                     aTGGTCAACCGCTATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCAt              <  1:2713869/69‑1 (MQ=255)
                                                     aTGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATAc                           >  1:1266766/1‑56 (MQ=255)
                                                      tGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCgg           <  1:1653794/71‑1 (MQ=255)
                                                      tGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCgg           <  1:3373798/71‑1 (MQ=255)
                                                      tGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCgg           <  1:264321/71‑1 (MQ=255)
                                                        gTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCAGCTTTACCGATACTTTCGAATTCCATCg            >  1:1617681/1‑68 (MQ=255)
                                                           aaCCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGa                              >  1:3054500/1‑47 (MQ=255)
                                                             ccGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCa    <  1:2973114/71‑1 (MQ=255)
                                                             ccGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCa    <  1:3942826/71‑1 (MQ=255)
                                                              cGCCATCGCCAGCTCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCaa   <  1:1788544/71‑1 (MQ=255)
                                                              cGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATc     >  1:3419062/1‑69 (MQ=255)
                                                              cGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCaa   <  1:1616148/71‑1 (MQ=255)
                                                              cGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCaa   <  1:3540335/71‑1 (MQ=255)
                                                               gCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCtt                                    >  1:4200219/1‑37 (MQ=255)
                                                               gCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCAAg  >  1:1043699/1‑71 (MQ=255)
                                                               gCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCAAg  >  1:2352545/1‑71 (MQ=255)
                                                               gCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCAAg  >  1:2672763/1‑71 (MQ=255)
                                                               gCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCAAg  >  1:3601337/1‑71 (MQ=255)
                                                                 |                                                                    
TCACGGGCGAAAAACTCTTCCAGGTTACGCACCAGCGACACCATGTTGATCTCATGGTCAACCGCCATCGCCAGCGCCGTACCCAGACGGCTGCCCGCTTTACCGATACTTTCGAATTCCATCGGCAGATCAAG  >  minE/1496496‑1496629

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