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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 833,168 T→C 20.5% G542G (GGT→GGC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE833,1680TC20.5% 149.9 / 34.0 78G542G (GGT→GGC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (30/32);  new base C (13/3);  total (43/35)
Fisher's exact test for biased strand distribution p-value = 2.41e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.87e-01

ATTCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCAACATGCTGATT  >  minE/833100‑833231
                                                                    |                                                               
attCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGc                                                               >  1:2310739/1‑71 (MQ=255)
 ttCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGc                                                               <  1:4779345/70‑1 (MQ=255)
 ttCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCg                                                              >  1:4875783/1‑71 (MQ=255)
 ttCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCg                                                              >  1:448964/1‑71 (MQ=255)
    ccATCGCCCGTGAATTTGCCGATACCGCCCATAAAACGCATGGGCGCTCGATGATTATCCTCGGCGCagg                                                            >  1:3470908/2‑70 (MQ=255)
       tCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCt                                                         >  1:5553360/1‑70 (MQ=255)
         gCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGa                                                       <  1:4305386/70‑1 (MQ=255)
          cccGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAAc                                                     <  1:1926014/71‑1 (MQ=255)
             gTGAATTTGCCGATACCGCCCATAAAACGCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCAc                                                  <  1:3346124/71‑1 (MQ=255)
               gAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTg                                                        <  1:2100598/63‑1 (MQ=255)
               gAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTg                                                        <  1:725909/63‑1 (MQ=255)
               gAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTg                                                >  1:3616516/1‑71 (MQ=255)
                aaTTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTg                                                        <  1:3599317/62‑1 (MQ=255)
                aaTTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTgg                                               >  1:3454848/1‑71 (MQ=255)
                 aTTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGt                                              <  1:5615322/71‑1 (MQ=255)
                    tggcGATACCGCCCATAAAACGCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTAt                                            >  1:5308718/4‑70 (MQ=255)
                    tGCCGATACCGCCCATAAAACGCATGGGCGCTCGATGATTATCCTCGGCGCaggtg                                                          >  1:964578/1‑54 (MQ=255)
                    tGCCGATACCGCCCATAAAACGCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCa                                                   >  1:3023558/1‑63 (MQ=255)
                    tGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTAt                                            >  1:2204781/1‑70 (MQ=255)
                         aTAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                      >  1:511904/1‑71 (MQ=255)
                         aTAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                      >  1:3836548/1‑71 (MQ=255)
                         aTAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                      >  1:2843909/1‑71 (MQ=255)
                         aTAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                      >  1:5594759/1‑71 (MQ=255)
                           aaCGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                      <  1:3817943/69‑1 (MQ=255)
                           aaCGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                      <  1:3811269/69‑1 (MQ=255)
                           aaCGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                      <  1:4694658/69‑1 (MQ=255)
                           aaCGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGa                                    >  1:3457660/1‑71 (MQ=255)
                            aCGCTGATAAAACGCACGGTCGTTCGATGATTATCGTAGGTGGGGGGCTGAACCACTGGTATCACCTc                                      <  1:5588011/68‑1 (MQ=255)
                             cGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCg                                     >  1:3274504/1‑68 (MQ=255)
                                 caTAAAACGCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGaa                              >  1:5055733/2‑71 (MQ=255)
                                  aTAAAACGCACGGTCGTTCGATGATTATCGTCGGt                                                                 >  1:5671122/1‑35 (MQ=255)
                                  aTAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGa                               <  1:988636/69‑1 (MQ=255)
                                  aTAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGa                               <  1:3246245/69‑1 (MQ=255)
                                  aTAAAACGCACGGTCGTTCGATGATTATCGTAGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAAc                             >  1:652935/1‑71 (MQ=255)
                                    aaaaCGCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTa                           >  1:5524510/1‑71 (MQ=255)
                                    aaaaCGCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTa                           >  1:5373823/1‑71 (MQ=255)
                                    aaaaCGCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTa                           >  1:2336230/1‑71 (MQ=255)
                                    aaaaCGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGGTGAACCACt                                                 >  1:3204065/1‑49 (MQ=255)
                                    aaaaCGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACt                            >  1:114290/1‑70 (MQ=255)
                                    aaaaCGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTa                           >  1:4628471/1‑71 (MQ=255)
                                    aaaaCGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTa                           >  1:3878286/1‑71 (MQ=255)
                                     aaaCGCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCAc                                         >  1:1484765/1‑56 (MQ=255)
                                     aaaCGCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCAc                                         >  1:1708728/1‑56 (MQ=255)
                                     aaaCGCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCAc                                         >  1:5116378/1‑56 (MQ=255)
                                       aCGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCg                        >  1:1316998/1‑71 (MQ=255)
                                        cGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGt                       >  1:669525/1‑71 (MQ=255)
                                          cACGGTCGTTCGATGATTATCGTCGGTGCGCGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTgg                     <  1:1004468/71‑1 (MQ=255)
                                           aCGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGt                    <  1:3815336/71‑1 (MQ=255)
                                              gTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACt                                                 <  1:3155028/39‑1 (MQ=255)
                                              gTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTc                   <  1:611356/69‑1 (MQ=255)
                                              gTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTc                   <  1:5667402/69‑1 (MQ=255)
                                              gTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTc                   <  1:1454271/69‑1 (MQ=255)
                                              gTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTc                   <  1:349528/69‑1 (MQ=255)
                                              gTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCt                  >  1:1401083/1‑70 (MQ=255)
                                              gTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTg                 <  1:1420865/71‑1 (MQ=255)
                                              gTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTg                 <  1:5611212/71‑1 (MQ=255)
                                               tCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGa                >  1:5689090/1‑71 (MQ=255)
                                               tCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGa                >  1:4611107/1‑71 (MQ=255)
                                                 gTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCg                        >  1:2467066/1‑61 (MQ=255)
                                                 gTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGAt               >  1:1571150/1‑70 (MQ=255)
                                                 gTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATc              <  1:2996689/71‑1 (MQ=255)
                                                 gTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATc              <  1:2989894/71‑1 (MQ=255)
                                                  ttCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGa                                    <  1:588702/48‑1 (MQ=255)
                                                  ttCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGa                                    <  1:5588474/48‑1 (MQ=255)
                                                  ttCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCa             <  1:5547149/71‑1 (MQ=255)
                                                  ttCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCa             <  1:1583912/71‑1 (MQ=255)
                                                    cGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCaa            >  1:1259031/1‑70 (MQ=255)
                                                    cGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCaa            >  1:5430147/1‑70 (MQ=255)
                                                    cGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTACCGCGGGATGATCaa            >  1:2968102/1‑70 (MQ=255)
                                                     gatgatTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTACCGCGGGATGATCaa            <  1:5499255/69‑1 (MQ=255)
                                                      atgatTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTACCGCGGGATGATCAatat         <  1:4954499/71‑1 (MQ=255)
                                                       tgatTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCaa            <  1:5172200/67‑1 (MQ=255)
                                                         atTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCAACATGc       <  1:3981034/70‑1 (MQ=255)
                                                          ttATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTACCGCGGGATGATCAATATGCt      >  1:4704277/1‑70 (MQ=255)
                                                             tcgtcgGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATc              >  1:1731914/1‑59 (MQ=255)
                                                             tcgtcgGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCa             >  1:5692257/1‑60 (MQ=255)
                                                             tcgtcgGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCAACATGCTGAtt  >  1:5324934/1‑71 (MQ=255)
                                                             tcgtcgGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCAACATGCTGAt   <  1:4684714/70‑1 (MQ=255)
                                                               gtcgGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTc                   <  1:3251542/52‑1 (MQ=255)
                                                                    |                                                               
ATTCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCAACATGCTGATT  >  minE/833100‑833231

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