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 832,118 T→C 20.2% I192I (ATT→ATC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,1180TC20.2% 173.8 / 39.4 89I192I (ATT→ATC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (38/33);  new base C (12/6);  total (50/39)
Fisher's exact test for biased strand distribution p-value = 4.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

ATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCGGTACTTGCTT  >  minE/832050‑832186
                                                                    |                                                                    
attgccgccGCTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATccc                                                                    <  1:3152349/68‑1 (MQ=255)
aTCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTcc                                                                    >  1:936587/1‑71 (MQ=255)
 tCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCg                                                                   >  1:2305049/1‑71 (MQ=255)
   gccgccGCTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGc                                                                 >  1:4053174/1‑71 (MQ=255)
   gccgccGCTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGc                                                                 >  1:634764/1‑71 (MQ=255)
   gccgcATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTCGCTGGTTTCTCGCCAATTCCGGc                                                                 <  1:2273519/71‑1 (MQ=255)
     cgcATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCaa                                                               >  1:123709/1‑71 (MQ=255)
       cATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATg                                                             <  1:5015116/71‑1 (MQ=255)
         tCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTc                                                                     <  1:4360545/61‑1 (MQ=255)
         tCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGc                                                                 <  1:2610061/65‑1 (MQ=255)
         tCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGc                                                                 <  1:993397/65‑1 (MQ=255)
         tCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTc                                                           >  1:4559810/1‑71 (MQ=255)
         gcTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGc                                                                 <  1:183876/64‑1 (MQ=255)
         gcTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTc                                                           <  1:5170591/70‑1 (MQ=255)
           tAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTcc                                                                    >  1:5432170/1‑60 (MQ=255)
           tAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGc                                                                 <  1:2670855/63‑1 (MQ=255)
            aaCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCg                                                          >  1:517407/1‑69 (MQ=255)
            aaCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGAt                                                        >  1:317158/1‑71 (MQ=255)
             aCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCg                                                                   <  1:3344827/59‑1 (MQ=255)
             aCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCaa                                                               >  1:2961017/1‑63 (MQ=255)
             aCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTc                                                           <  1:3704031/67‑1 (MQ=255)
             aCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTc                                                           <  1:2022767/67‑1 (MQ=255)
               gTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGt                                                     >  1:1435766/1‑71 (MQ=255)
                 ttACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGtt                                                    >  1:3071241/1‑70 (MQ=255)
                  tACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATg                                                             >  1:3673520/1‑60 (MQ=255)
                  tACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGttt                                                   <  1:2123143/70‑1 (MQ=255)
                  tACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGttt                                                   <  1:3578637/70‑1 (MQ=255)
                    gacCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGTTTCt                                                 >  1:1141376/2‑70 (MQ=255)
                    cacCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCtt                                                <  1:1033628/71‑1 (MQ=255)
                    cacCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCt                                                 <  1:3327177/70‑1 (MQ=255)
                       cATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCtt                                                >  1:15918/1‑68 (MQ=255)
                       cATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                                               >  1:64348/1‑69 (MQ=255)
                       cATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCAGGCAATGTCGATGGTTTCTTACg                                             >  1:89437/1‑71 (MQ=255)
                        aTCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATgg                                                      <  1:3825966/61‑1 (MQ=255)
                        aTCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGTTTc                                                  <  1:4413210/65‑1 (MQ=255)
                         tCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGTTTCTTACGcc                                           >  1:4959062/1‑70 (MQ=255)
                         tCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTc                                                                     <  1:4729009/45‑1 (MQ=255)
                         tCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCa                                           >  1:4398508/1‑71 (MQ=255)
                         tCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCa                                           <  1:4060976/71‑1 (MQ=255)
                         tCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCa                                           >  1:687530/1‑71 (MQ=255)
                           aaaacCTACGGCCCGGATCGCGTTGCCGGTATCTCGCCGATCCCGGCGATGTCGATGGTTTCTTACGccgc                                         >  1:5204152/1‑68 (MQ=255)
                           aaaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                                               >  1:4345175/1‑65 (MQ=255)
                           aaaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                                               >  1:911313/1‑65 (MQ=255)
                           aaaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                                               >  1:4121883/1‑65 (MQ=255)
                           aaaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCAt                                          <  1:2540267/70‑1 (MQ=255)
                            aaacCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGcga                                                               >  1:12496/1‑46 (MQ=255)
                            aaacCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGa                                                         >  1:5329077/1‑54 (MQ=255)
                            aaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATgg                                                      >  1:4079964/1‑57 (MQ=255)
                            aaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATgg                                                      >  1:105675/1‑57 (MQ=255)
                             aaaCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCgg                                                                  >  1:141378/1‑44 (MQ=25)
                                      cccGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACg                                >  1:3754798/1‑69 (MQ=255)
                                       ccGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCt                              >  1:1641594/1‑70 (MQ=255)
                                          gACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCa                                           <  1:4593028/54‑1 (MQ=255)
                                            ccGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTAtctct                        >  1:3760901/1‑71 (MQ=255)
                                             cGTGTTGCTGGTTTCTCTCCAATTCCGGCAATGTCGATGGTTTCt                                                 <  1:5041481/45‑1 (MQ=255)
                                             cGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCt                                                 <  1:4416514/45‑1 (MQ=255)
                                             cGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTAtctctc                       <  1:432230/71‑1 (MQ=255)
                                               tgtTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                                               >  1:2281001/1‑45 (MQ=255)
                                               tgtTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                                               >  1:4226510/1‑45 (MQ=255)
                                               tgtTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCg                      >  1:5561017/1‑70 (MQ=255)
                                               tgtTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCg                      >  1:4606854/1‑70 (MQ=255)
                                                 ttGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCAt                                          <  1:4333045/48‑1 (MQ=255)
                                                 ttGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCAt                                          <  1:3673273/48‑1 (MQ=255)
                                                 ttGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCt                    >  1:2834931/1‑70 (MQ=255)
                                                 ttGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTg                   <  1:4234690/71‑1 (MQ=255)
                                                   gCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGc                     >  1:4435639/1‑67 (MQ=255)
                                                    cTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCtt                                                <  1:3528944/39‑1 (MQ=255)
                                                     cggTTTCTCGCCGATCCCGGCGATGTCGATGGTTTCTTACGCCGCCGGAACGCGTTATCTGTCGCTGCTTg               <  1:5681275/70‑1 (MQ=255)
                                                     cggTTTCTCGCCGATCCCGGCGATGTCGATGGTTTCTTACGCCGCCGGAACGCGTTATCTGTCGCTGCTTg               <  1:4056302/70‑1 (MQ=255)
                                                      ggTTTCTCGCCGATCCCGGCGATGTCGATGGTTTCTTACGCCGCCGGAACGCGTTATCTGTCGCTGCTTgg              >  1:3516300/1‑71 (MQ=255)
                                                         ttCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCgg           >  1:797299/1‑71 (MQ=255)
                                                         ttCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCgg           >  1:309090/1‑71 (MQ=255)
                                                          tctcGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCgg           >  1:5516512/1‑70 (MQ=255)
                                                              gCCGATCCCGGCGATGTCGATGGTTTCTTACGCCGCCGGAACGCGTTATCTGTCGCTgct                 >  1:3490314/1‑58 (MQ=255)
                                                              gCCGATCCCGGCGATGTCGATGGTTTCTTACGCCGCCGGAACGCGTTATCTGTCGCTgct                 >  1:5337072/1‑58 (MQ=255)
                                                              gCCGATCCCGGCGATGTCGATGGTTTCTTACGCCGCCGGAACGCGTTATCTGTCGCTgct                 >  1:907774/1‑58 (MQ=255)
                                                              gCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGc                               <  1:4074580/46‑1 (MQ=255)
                                                              gCCAATTCCGGCAACGTCGATGGTTTCTTACGCATCGGGTGCACGc                               <  1:5222526/46‑1 (MQ=255)
                                                                cAATTCCGGCAATGTCGATGGTTTCTTACGCATCggg                                      >  1:4835259/1‑37 (MQ=255)
                                                                cAATTCCGGCAATGTCGATGGTTTCTTACGCATCg                                        >  1:832534/1‑35 (MQ=255)
                                                                cAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGc                               >  1:2409515/1‑44 (MQ=255)
                                                                 aaTTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTg               <  1:5503313/59‑1 (MQ=255)
                                                                 aaTTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTg               <  1:5495926/59‑1 (MQ=255)
                                                                 aaTTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTg               <  1:1481988/59‑1 (MQ=255)
                                                                 aaTTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTg               <  1:110474/59‑1 (MQ=255)
                                                                  aTTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCGGTACt       <  1:927527/66‑1 (MQ=255)
                                                                  aTTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCGGTACTTGCtt  <  1:4752251/71‑1 (MQ=255)
                                                                  aTTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCGGTACTTGCtt  <  1:3642011/71‑1 (MQ=255)
                                                                  aTTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCGGTACTTGCt   >  1:4678871/1‑70 (MQ=255)
                                                                  aTTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCGGTACTTGCt   >  1:4341106/1‑70 (MQ=255)
                                                                   ttCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGAt                 >  1:898989/1‑55 (MQ=255)
                                                                   ttCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGAt                 >  1:3654107/1‑55 (MQ=255)
                                                                    tCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCGGTACTTGCtt  <  1:5452763/69‑1 (MQ=255)
                                                                    |                                                                    
ATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCGCTGATTGGCGGTACTTGCTT  >  minE/832050‑832186

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