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 2,919,357 A→C 21.9% I113M (ATT→ATG) ‡ argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,3570AC21.9% 210.1 / 84.9 137I113M (ATT→ATG) ‡argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base A (59/48);  new base C (18/12);  total (77/60)
Fisher's exact test for biased strand distribution p-value = 6.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.98e-01

Only 100 of 147 total aligned reads displayed.

CGTGGGATGGAACTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAA  >  minE/2919288‑2919427
                                                                     |                                                                      
cGTGGGATGGAACTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACaa                                                                       <  1:4943226/71‑1 (MQ=255)
cGTGGGATGGAACTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACa                                                                        <  1:1013121/70‑1 (MQ=255)
cGTGGGATGGAACTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACa                                                                        <  1:5410958/70‑1 (MQ=255)
 gTGGGATGGAACTCATTGGTCAGGCCATTCCATACGGGCACGCTAGCGTATTCCGCCAGTGTTTCGACa                                                                        <  1:980047/69‑1 (MQ=255)
  tGGGATGGAACTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAAtc                                                                     <  1:4858629/71‑1 (MQ=255)
       tGGAACTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCt                                                                 >  1:2501416/1‑70 (MQ=255)
       tGGAACTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCt                                                                 >  1:4717303/1‑70 (MQ=255)
         gAACTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGAc                                                              >  1:1907166/1‑71 (MQ=255)
            cTCGTTGGTCAGCCCGTTCCACACCGGCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGccgt                                                           <  1:2124962/71‑3 (MQ=255)
            cTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCAt                                                           <  1:3328650/71‑1 (MQ=255)
            cTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCAt                                                           <  1:1589782/71‑1 (MQ=255)
               aTTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAAtctc                                                                   >  1:4668015/1‑60 (MQ=255)
               aTTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGc                                                        >  1:5674693/1‑71 (MQ=255)
               aTTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGc                                                        >  1:5324878/1‑71 (MQ=255)
                 tGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGa                                                               >  1:3549004/1‑62 (MQ=255)
                  ggTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAAtc                                                                     >  1:4569142/1‑55 (MQ=255)
                  ggTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAAtc                                                                     >  1:1910597/1‑55 (MQ=255)
                   gTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCcgc                                                     <  1:2879803/70‑1 (MQ=255)
                   gTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCcgc                                                     <  1:2973416/70‑1 (MQ=255)
                   gTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCcgc                                                     <  1:571441/70‑1 (MQ=255)
                   gTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCcgc                                                     <  1:4780463/70‑1 (MQ=255)
                    tCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGa                                                   <  1:3589598/71‑1 (MQ=255)
                      aGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGAt                                                  <  1:3962260/70‑1 (MQ=255)
                      aGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATa                                                 >  1:2758018/1‑71 (MQ=255)
                       ggCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATa                                                          <  1:4341432/61‑1 (MQ=255)
                       ggCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGa                                                   <  1:241723/68‑1 (MQ=255)
                        gCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCa                                                            <  1:900757/58‑1 (MQ=255)
                        gCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACt                                               <  1:1812446/71‑1 (MQ=255)
                         ccgttCCACACCGGCACGCCCGCATACTGCGCCAGCGGTTCGACCACTTCCTGGCCGTGACCGCGATACTg                                              <  1:4983946/68‑1 (MQ=255)
                         ccATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTg                                              <  1:1675769/71‑1 (MQ=255)
                          cATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGa                                             <  1:4742506/71‑1 (MQ=255)
                           gttCCACACCGGCACGCCCGCATACTGCGCCAGCGTATCGACCACTTCCTGGCCGTGACCGCGATACTg                                              <  1:1508771/68‑1 (MQ=255)
                            ttCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGa                                                   <  1:3283864/63‑1 (MQ=255)
                              ccATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATAc                                         >  1:5014182/1‑71 (MQ=255)
                              ccATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATAc                                         >  1:402945/1‑71 (MQ=255)
                              ccATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATAc                                         >  1:2680694/1‑71 (MQ=255)
                              ccACACCGGCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAAtgc                                         >  1:3211553/1‑69 (MQ=255)
                               cATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATa                                          <  1:4792160/69‑1 (MQ=255)
                               cATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATAcc                                        >  1:5485464/1‑71 (MQ=255)
                                aTACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCg                                       <  1:2367806/71‑1 (MQ=255)
                                aTACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCg                                       <  1:1697541/71‑1 (MQ=255)
                                  aCCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACaa                                                                       >  1:2500805/1‑37 (MQ=255)
                                  aCCGGCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGt                                      >  1:733439/1‑70 (MQ=255)
                                  aCCGGCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGt                                      >  1:1745219/1‑70 (MQ=255)
                                   ccGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTc                                     <  1:3940701/70‑1 (MQ=255)
                                   ccGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCa                                    >  1:4518782/1‑71 (MQ=255)
                                   ccGGCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCa                                    >  1:2263157/1‑71 (MQ=255)
                                     ggCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                  >  1:3176107/1‑71 (MQ=255)
                                     ggCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                  >  1:4488857/1‑71 (MQ=255)
                                     ggCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                  <  1:2234140/71‑1 (MQ=255)
                                      gCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATAc                                 <  1:3546077/71‑1 (MQ=255)
                                      gCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                  >  1:5183585/1‑70 (MQ=255)
                                      gCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                  >  1:484841/1‑70 (MQ=255)
                                      gCACGCCCGCATACTGCGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATa                                  >  1:269145/1‑70 (MQ=255)
                                       cACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACa                                >  1:10161/1‑71 (MQ=255)
                                          gCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCt                                                                 >  1:1112475/1‑35 (MQ=255)
                                          gCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATa                                                 >  1:3112073/1‑51 (MQ=255)
                                          gCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGc                             <  1:3089849/71‑1 (MQ=255)
                                           cTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGc                             >  1:78385/1‑70 (MQ=255)
                                           cTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCg                            <  1:5055038/71‑1 (MQ=255)
                                              gCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGa                           <  1:5155006/69‑1 (MQ=255)
                                                gTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGAcc                         >  1:4983560/1‑69 (MQ=255)
                                                 tATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAg                      >  1:4119429/1‑71 (MQ=255)
                                                 tATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAg                      >  1:2112056/1‑71 (MQ=255)
                                                  aTTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAg                      >  1:776690/1‑70 (MQ=255)
                                                  aTTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAg                      <  1:133222/70‑1 (MQ=255)
                                                  aTTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAg                      >  1:1579204/1‑70 (MQ=255)
                                                   ttCCGCCAGTGTTTCGACAATCTCCTGACCATAGcc                                                       >  1:4921986/1‑36 (MQ=255)
                                                   ttCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGaa                                            >  1:1573367/1‑47 (MQ=255)
                                                   ttCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCa                                    >  1:1888607/1‑55 (MQ=255)
                                                   ttCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCa                                    >  1:2796713/1‑55 (MQ=255)
                                                     ccGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCAc                   <  1:74845/70‑1 (MQ=255)
                                                      cGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACa                                >  1:975375/1‑56 (MQ=255)
                                                      cGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTTAATGCCGTCATACATCCGCCCGAGAAc                   <  1:383035/69‑1 (MQ=255)
                                                      cGCCAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACATCCGCCCGAGAAc                   <  1:1889663/69‑1 (MQ=255)
                                                       gCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGt                                      <  1:305113/49‑1 (MQ=255)
                                                         cAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCa                                    >  1:1321866/1‑49 (MQ=255)
                                                         cAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCa                                    >  1:550620/1‑49 (MQ=255)
                                                         cAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCggg              <  1:4073582/71‑1 (MQ=255)
                                                         cAGCGTTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACATCCGCCCGAGAAcccgcg              <  1:4149179/71‑3 (MQ=255)
                                                          agcgtTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACATCCGCCCGAGAACCCgcgc             <  1:2994542/68‑1 (MQ=255)
                                                          agcgtTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACATCCGCCCGAGAACCCgcgc             <  1:1399009/68‑1 (MQ=255)
                                                           gtgtTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCggg              >  1:846323/1‑69 (MQ=255)
                                                           gtgtTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCggg              >  1:1392164/1‑69 (MQ=255)
                                                           gtgtTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCggg              >  1:3615736/1‑69 (MQ=255)
                                                            cgtTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACATCCGCCCGAGAACCCgcgcgg           >  1:1599345/2‑69 (MQ=255)
                                                             gtTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACAtc                              >  1:4166330/1‑50 (MQ=255)
                                                             gtTTCGACCACTTCCTGGCCGTGACCGCGATACTGAATGCCGTCATACATCCGCCCGAgaa                    >  1:2348327/1‑59 (MQ=255)
                                                             gtTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAgt          >  1:115740/1‑71 (MQ=255)
                                                              tttCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGa                           <  1:3460941/53‑1 (MQ=255)
                                                              tttCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGa                           <  1:1687128/53‑1 (MQ=255)
                                                              tttCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGa                           <  1:4010447/53‑1 (MQ=255)
                                                              tttCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAgtg         >  1:261763/1‑71 (MQ=255)
                                                              tttCGACAATCTCCTGACAATAGCCGCGATACTGAATACCGTCATAc                                 <  1:1045940/47‑1 (MQ=255)
                                                                tCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCaa                       >  1:4513022/1‑55 (MQ=255)
                                                                tCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTc       >  1:4688723/1‑71 (MQ=255)
                                                                 cGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCa                    >  1:3830768/1‑57 (MQ=255)
                                                                  gACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCtt     <  1:2301822/71‑1 (MQ=255)
                                                                    cAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCa                    >  1:5171538/1‑54 (MQ=255)
                                                                     aaTCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTaa  <  1:1606965/71‑1 (MQ=255)
                                                                     |                                                                      
CGTGGGATGGAACTCATTGGTCAGGCCATTCCATACCGGCACGCTAGCGTATTCCGCCAGTGTTTCGACAATCTCCTGACCATAGCCGCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAA  >  minE/2919288‑2919427

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