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 R2 230 93.6 4701257 96.3% 4527310 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 627,979 A→G 43.0% K143K (AAA→AAG)  kdsB → 3‑deoxy‑manno‑octulosonate cytidylyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE627,9790AG43.0% 28.0 / 97.8 79K143K (AAA→AAG) kdsB3‑deoxy‑manno‑octulosonate cytidylyltransferase
Reads supporting (aligned to +/- strand):  ref base A (26/19);  new base G (21/13);  total (47/32)
Fisher's exact test for biased strand distribution p-value = 8.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

GTGGGTATGGCGACTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTGGGATCGTGATCGT  >  minE/627911‑628048
                                                                    |                                                                     
gTGGGTATGGCGACTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGt                                                                     <  1:1085117/71‑1 (MQ=255)
 tGGGTATGGCGACTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTg                                                                    <  1:1623309/71‑1 (MQ=255)
      aTGGCGACTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTtct                                                               >  1:481119/1‑71 (MQ=255)
      aTGGCGACTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTCGTtct                                                               >  1:1555127/1‑71 (MQ=255)
       tGGCGACTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTACCCCGAATGCGGTGAAAGTGGTtctc                                                              >  1:3438118/1‑71 (MQ=255)
       tGGCGACTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTtctc                                                              >  1:1707587/1‑71 (MQ=255)
         gCGACTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGa                                                            >  1:4589547/1‑71 (MQ=255)
         gCGACTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGa                                                            >  1:186353/1‑71 (MQ=255)
            aCTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGc                                                         >  1:1016922/1‑71 (MQ=255)
             ctctGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCt                                                        >  1:2654955/1‑71 (MQ=255)
             ctctGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCt                                                        <  1:2388770/71‑1 (MQ=255)
             ctctGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCt                                                        <  1:4168519/71‑1 (MQ=255)
              tctGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCt                                                        >  1:1288850/1‑70 (MQ=255)
              tctGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCt                                                        >  1:461656/1‑70 (MQ=255)
              tctGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTtct                                                               >  1:483419/1‑63 (MQ=255)
                tGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGtt                                                                 >  1:2147310/1‑59 (MQ=255)
                tGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTg                                                       <  1:4105024/69‑1 (MQ=255)
                tGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTg                                                       >  1:2714825/1‑69 (MQ=255)
                tGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTg                                                       <  1:2985946/69‑1 (MQ=255)
                 ggCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAg                                                    >  1:1554114/1‑71 (MQ=255)
                  gCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTTAAGGTGGTTCTCGACGCTGa                                                      <  1:1246828/68‑1 (MQ=255)
                  gCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGa                                                      <  1:4067480/68‑1 (MQ=255)
                  gCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAgg                                                   <  1:1107765/71‑1 (MQ=255)
                  gCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAgg                                                   <  1:4208130/71‑1 (MQ=255)
                  gCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAg                                                    <  1:1828517/70‑1 (MQ=255)
                  gCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAg                                                    <  1:1818694/70‑1 (MQ=255)
                   cGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAggg                                                  <  1:2204110/71‑1 (MQ=255)
                       gCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGa                                                            >  1:3004737/1‑57 (MQ=255)
                       gCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAgtgt                                                 >  1:30175/1‑68 (MQ=255)
                         cAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCa                                            >  1:2817940/1‑71 (MQ=255)
                           aTCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACt                                          >  1:1527459/1‑71 (MQ=255)
                            tCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGt                                                                     <  1:356618/43‑1 (MQ=255)
                            tCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTg                                         <  1:3353788/71‑1 (MQ=255)
                            tCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAg                                                                      >  1:847019/1‑42 (MQ=255)
                            tCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTg                                         <  1:4488498/71‑1 (MQ=255)
                            tCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTg                                         <  1:3075254/71‑1 (MQ=255)
                             ccACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGa                                                            >  1:4249343/1‑51 (MQ=255)
                             ccACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGa                                                            >  1:941635/1‑51 (MQ=255)
                              cacaATGCGGAAGAAGCGTTTAACCCGAATGCGGTGTAAGTGGTTCTCGACGCTGAAGGGTATGCACTGt                                        >  1:1512201/1‑70 (MQ=255)
                              cacaATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGa                                                            >  1:900989/1‑50 (MQ=255)
                              cacaATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTa                                       >  1:2691506/1‑71 (MQ=255)
                              cacaATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTa                                       >  1:1527001/1‑71 (MQ=255)
                              cacaATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAg                                                                      >  1:3283871/1‑40 (MQ=255)
                              cacaATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAg                                                                      >  1:4562840/1‑40 (MQ=255)
                              cacaATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCt                                                        >  1:4648926/1‑54 (MQ=255)
                              cacaATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTa                                       <  1:1061218/71‑1 (MQ=255)
                               acaATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTAc                                      <  1:1403299/71‑1 (MQ=255)
                                caATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTa                                                >  1:646819/1‑60 (MQ=255)
                                  aTGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAggg                                                  <  1:2494427/56‑1 (MQ=255)
                                    gCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTtctc                                 >  1:2314809/1‑71 (MQ=255)
                                    gCGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTtct                                  >  1:2869378/1‑70 (MQ=255)
                                     cGGAAGAAGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTtctct                                <  1:906821/71‑1 (MQ=255)
                                     cGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGAc                                                           >  1:4034812/1‑44 (MQ=255)
                                       gaagaaGCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTg                                         <  1:1156110/60‑1 (MQ=255)
                                         agaagCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTcgcg                            >  1:3164029/1‑71 (MQ=255)
                                             gCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGccac                        <  1:3027150/71‑1 (MQ=255)
                                             gCGTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGccac                        <  1:2335257/71‑1 (MQ=255)
                                             gCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGa                                                            >  1:1877821/1‑35 (MQ=255)
                                               gTTTAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGccacca                      >  1:3937146/1‑71 (MQ=255)
                                                tttAACCCGAATGCGGTTAAAGTGTTTCTCGACGCTGAAGGGTa                                                >  1:4477417/1‑44 (MQ=38)
                                                tttAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCAt                     >  1:1155330/1‑71 (MQ=255)
                                                tttAACCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCAt                     >  1:2877235/1‑71 (MQ=255)
                                                tttAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTg                                                       <  1:2672855/37‑1 (MQ=255)
                                                   aaCCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTc                   <  1:879896/70‑1 (MQ=255)
                                                    aCCCGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCt                 <  1:1176173/71‑1 (MQ=255)
                                                     cccGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCa                                            <  1:1397576/43‑1 (MQ=255)
                                                      ccGAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGccacca                      >  1:2975506/1‑64 (MQ=255)
                                                      ccGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTg               >  1:1717564/1‑71 (MQ=255)
                                                        gAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACt                                          <  1:1644941/42‑1 (MQ=255)
                                                        gAATGCGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTa                                       >  1:4420668/1‑45 (MQ=255)
                                                        gAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTgg              >  1:2843565/1‑70 (MQ=255)
                                                        gAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTgg              >  1:3418123/1‑70 (MQ=255)
                                                        gAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTgg              >  1:3518875/1‑70 (MQ=255)
                                                             cGGTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTAc                                      >  1:1133273/1‑41 (MQ=255)
                                                              ggTGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTGGgatcgt        <  1:2071640/70‑1 (MQ=255)
                                                              ggTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTGGgatcgtg       <  1:2018996/71‑1 (MQ=255)
                                                               gTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTGGgatcgtga      <  1:649597/71‑1 (MQ=255)
                                                                tGAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTGGgatcgtgat     >  1:2524759/1‑71 (MQ=255)
                                                                 gAAGGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTGGgatcgtgatc    >  1:1528790/1‑71 (MQ=255)
                                                                  aaaGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTtc                                   >  1:4242407/1‑39 (MQ=255)
                                                                   aaGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTGGgatcgtgatcgt  <  1:468532/71‑1 (MQ=255)
                                                                    aGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTtct                                  <  1:3833618/38‑1 (MQ=255)
                                                                    |                                                                     
GTGGGTATGGCGACTCTGGCGGTGCCAATCCACAATGCGGAAGAAGCGTTTAACCCGAATGCGGTGAAAGTGGTTCTCGACGCTGAAGGGTATGCACTGTACTTCTCTCGCGCCACCATTCCTTGGGATCGTGATCGT  >  minE/627911‑628048

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