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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,918,727 A→C 12.5% T323T (ACT→ACG)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,918,7270AC12.5% 117.9 / 15.1 56T323T (ACT→ACG) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base A (28/21);  new base C (4/3);  total (32/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.32e-01

TTTGTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCTCATCAGT  >  minE/2918657‑2918792
                                                                      |                                                                 
tttGTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATa                                                                   <  1:3044818/71‑1 (MQ=255)
  tGTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAg                                                                  >  1:192211/1‑70 (MQ=255)
   gTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGt                                                                 <  1:3293525/70‑1 (MQ=255)
   gTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGt                                                                 <  1:1400638/70‑1 (MQ=255)
   gTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGt                                                                 <  1:290428/70‑1 (MQ=255)
    tATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAg                                                                  <  1:427559/68‑1 (MQ=255)
    tATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAt                                                               >  1:1619529/1‑71 (MQ=255)
          ccGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATa                                                          <  1:3155333/70‑1 (MQ=255)
            ggCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACg                                                        >  1:1256403/1‑70 (MQ=255)
               aTCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGttt                                                    <  1:2928845/71‑1 (MQ=255)
               aTCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGttt                                                    <  1:2762301/71‑1 (MQ=255)
                 cTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTc                                                  >  1:623347/1‑71 (MQ=255)
                  tttATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATa                                                                   >  1:3405513/1‑53 (MQ=255)
                  tttATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTcc                                                 >  1:1111846/1‑71 (MQ=255)
                  tttATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTcc                                                 >  1:879681/1‑71 (MQ=255)
                   ttATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTa                                                                >  1:2092705/1‑55 (MQ=255)
                      taGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCt                                             <  1:537347/71‑1 (MQ=255)
                       aGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCt                                             >  1:516079/1‑70 (MQ=255)
                        gCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATa                                                                   <  1:1278792/47‑1 (MQ=255)
                             aGCAATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCaa                                       >  1:2296540/1‑70 (MQ=255)
                             aGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCaa                                       >  1:368211/1‑70 (MQ=255)
                             aGCAATTATTTACTGAGCGTCGAGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCaa                                       >  1:1151857/1‑70 (MQ=255)
                              gCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCaaaa                                     <  1:1594911/71‑1 (MQ=255)
                               cAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTa                                                                >  1:3683234/1‑43 (MQ=255)
                                 attattTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACa                                  <  1:2201761/71‑1 (MQ=255)
                                 attattTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACa                                  <  1:1452984/71‑1 (MQ=255)
                                   tattTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGc                                               >  1:210804/1‑56 (MQ=255)
                                    attTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAAt                                >  1:1688317/1‑70 (MQ=255)
                                       tACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCt                             <  1:3499375/70‑1 (MQ=255)
                                       tACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTg                            >  1:1084860/1‑71 (MQ=255)
                                       tACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTg                            >  1:3032873/1‑71 (MQ=255)
                                       tACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTg                            >  1:795772/1‑71 (MQ=255)
                                        aCTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCt                                             >  1:2843328/1‑53 (MQ=255)
                                        aCTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTg                            <  1:609998/70‑1 (MQ=255)
                                          tGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCaa                                       <  1:2005096/57‑1 (MQ=255)
                                          tGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTggcg                         >  1:1903999/1‑71 (MQ=255)
                                          caaGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTcgcc                         >  1:527391/3‑70 (MQ=255)
                                           aaGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTcgccg                        >  1:1215440/2‑69 (MQ=255)
                                            aGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTcg                                        <  1:1579608/54‑2 (MQ=255)
                                            aGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTggcgg                        >  1:1836579/1‑70 (MQ=255)
                                            aGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTggcgg                        <  1:3623585/70‑1 (MQ=255)
                                             gCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTg                                            <  1:1589865/49‑1 (MQ=255)
                                                tCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGAt                   <  1:2444571/71‑1 (MQ=255)
                                                  gcgACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTc                 >  1:1460201/1‑71 (MQ=255)
                                                   cgACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTc                 >  1:1284918/1‑70 (MQ=255)
                                                     aCCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCg                >  1:3350507/1‑69 (MQ=255)
                                                      tcATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGAt                                >  1:2305279/2‑52 (MQ=255)
                                                       cATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTcgccgccg                     >  1:511659/1‑60 (MQ=255)
                                                        aTCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCaaaca            <  1:2276540/70‑3 (MQ=255)
                                                         tCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGa               <  1:2097934/66‑1 (MQ=255)
                                                            ccGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCtca       <  1:538164/71‑1 (MQ=255)
                                                             cGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGa            >  1:1843292/1‑65 (MQ=255)
                                                             cGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTcg                                        <  1:3110759/37‑2 (MQ=16)
                                                              gCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCtcat      >  1:2259504/1‑70 (MQ=255)
                                                              gCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCtcat      >  1:2800896/1‑70 (MQ=255)
                                                                 ttGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCTCATCAg   >  1:2546262/1‑70 (MQ=255)
                                                                  tGATAGTATGCATACGGTTTTCCGCCTGATCAAAAAc                                   <  1:1141652/37‑1 (MQ=255)
                                                                  tGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCACATCAGt  >  1:2475180/1‑70 (MQ=255)
                                                                  tGATAGTATGCATACGGTTTTCCACCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCTCATCAGt  <  1:1433903/70‑1 (MQ=255)
                                                                      |                                                                 
TTTGTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCTCATCAGT  >  minE/2918657‑2918792

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