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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,819,774 G→T 26.1% P61P (CCG→CCT)  nrfD → formate‑dependent nitrite reductase, membrane subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,819,7740GT26.1% 129.4 / 35.9 80P61P (CCG→CCT) nrfDformate‑dependent nitrite reductase, membrane subunit
Reads supporting (aligned to +/- strand):  ref base G (42/17);  new base T (10/11);  total (52/28)
Fisher's exact test for biased strand distribution p-value = 6.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCGTGGACCT  >  minE/2819729‑2819832
                                             |                                                          
cggTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:289270/1‑69 (MQ=255)
cggTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     <  1:514620/69‑1 (MQ=255)
cggTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     <  1:2172518/69‑1 (MQ=255)
cggTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:2181779/1‑69 (MQ=255)
cggTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     <  1:468143/69‑1 (MQ=255)
cggTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:2402988/1‑69 (MQ=255)
cggTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:1279061/1‑69 (MQ=255)
cggTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     <  1:1274438/69‑1 (MQ=255)
cggTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:2860247/1‑69 (MQ=255)
cggTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGGCTGtt                                     <  1:385818/69‑1 (MQ=255)
          aGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGt                            >  1:268567/1‑68 (MQ=255)
          aGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTc                           >  1:2634067/1‑69 (MQ=255)
          aGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTc                           >  1:443343/1‑69 (MQ=255)
          aGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTc                           >  1:644374/1‑69 (MQ=255)
             aCGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTg                                    >  1:2278272/1‑57 (MQ=255)
             aCGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTg                                    >  1:367194/1‑57 (MQ=255)
             aCGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTg                                    >  1:3201879/1‑57 (MQ=255)
             aCGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTg                                    >  1:208764/1‑57 (MQ=255)
             aCGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTg                                    >  1:656609/1‑57 (MQ=255)
             aCGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTg                                    >  1:1262180/1‑57 (MQ=255)
             aCGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTg                                    >  1:969256/1‑57 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGAt                                                 >  1:3371334/1‑43 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:593510/1‑55 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:113561/1‑55 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:217035/1‑55 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:3274432/1‑55 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:1826894/1‑55 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:593690/1‑55 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:3247544/1‑55 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:804075/1‑55 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGtt                                     >  1:2402464/1‑55 (MQ=255)
              cGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTCtt                                     >  1:1084668/1‑55 (MQ=255)
                ttGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCAc                     <  1:2753658/69‑1 (MQ=255)
                ttGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCAc                     <  1:501492/69‑1 (MQ=255)
                ttGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCAc                     <  1:1927294/69‑1 (MQ=255)
                ttGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCAc                     <  1:1949782/69‑1 (MQ=255)
                 tgctgcGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTg                                       >  1:396812/1‑50 (MQ=255)
                 tgctgcGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCAc                     >  1:2915136/1‑68 (MQ=255)
                 tgctgcGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCAc                     >  1:1989992/1‑68 (MQ=255)
                 tgctgcGCACCACGCTGATTGTAGGGCAGGGCGCGGTGATc                                                >  1:1264294/1‑41 (MQ=38)
                  gctgcGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCt                   >  1:2536590/1‑69 (MQ=255)
                  gctgcGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCt                   >  1:804309/1‑69 (MQ=255)
                  gctgcGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCt                   >  1:615576/1‑69 (MQ=255)
                  gctgcGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCt                   >  1:2862629/1‑69 (MQ=255)
                  gctgcGCACCACGCTGATTGTCGGG‑‑GGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTg                  >  1:1993996/1‑68 (MQ=255)
                       gcACCACGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTc                           >  1:947704/1‑56 (MQ=255)
                       gcACCACGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACaa              >  1:3277450/1‑69 (MQ=255)
                       gcACCACGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACaa              >  1:1078447/1‑69 (MQ=255)
                       gcACCACGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACaa              >  1:3213815/1‑69 (MQ=255)
                       gcACCACGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACaa              >  1:977284/1‑69 (MQ=255)
                       gcACCACGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACaa              >  1:3138767/1‑69 (MQ=255)
                       gcACCACGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACaa              >  1:2119469/1‑69 (MQ=255)
                       gcACCACGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACaa              >  1:2831005/1‑69 (MQ=255)
                       gcACCACGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACaa              >  1:1275966/1‑69 (MQ=255)
                       gcACCACGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACa               >  1:1834343/1‑68 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:1332321/43‑1 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:1386317/43‑1 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:1630478/43‑1 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:2013121/43‑1 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:1288524/43‑1 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:2373984/43‑1 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:2722270/43‑1 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:2991410/43‑1 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:3149366/43‑1 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:3102595/43‑1 (MQ=255)
                           cacGCTGATTGTCGGGCCTGGCGCGGTGATCCTCGGTCTGTTg                                    <  1:3160476/43‑1 (MQ=255)
                            acGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCg         >  1:2382523/1‑69 (MQ=255)
                            acGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCg         >  1:442605/1‑69 (MQ=255)
                            acGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCg         >  1:1994877/1‑69 (MQ=255)
                            acGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCg         >  1:1811370/1‑69 (MQ=255)
                            acGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCg         >  1:714512/1‑69 (MQ=255)
                              gCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCGTg       <  1:2961849/69‑1 (MQ=255)
                              gCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCGTg       <  1:3221748/69‑1 (MQ=255)
                               cTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCGTgg      >  1:256129/1‑69 (MQ=255)
                                    tGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCGTGGACCt  <  1:714110/68‑1 (MQ=255)
                                     gTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGAc                <  1:1122831/53‑1 (MQ=255)
                                     gTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGAc                <  1:868089/53‑1 (MQ=255)
                                     gTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGAc                <  1:2195064/53‑1 (MQ=255)
                                     gTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGAc                <  1:2377585/53‑1 (MQ=255)
                                     gTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGAc                <  1:3094259/53‑1 (MQ=255)
                                             |                                                          
CGGTGCAGACAGTACGTTGCTGCGCACCACGCTGATTGTCGGGCCGGGCGCGGTGATCCTCGGTCTGTTGATCCTCGTCTTCCACCTGACAAGACCGTGGACCT  >  minE/2819729‑2819832

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A