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
A3 F2 I1 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 Exported 609,739 G→C 26.8% A172G (GCA→GGA) ‡ pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported609,7390GC26.8% 209.7 / 82.9 123A172G (GCA→GGA) ‡pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base G (58/32);  new base C (14/19);  total (72/51)
Fisher's exact test for biased strand distribution p-value = 3.86e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.47e-01

Only 100 of 123 total aligned reads displayed.

TCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACA  >  Exported/609671‑609808
                                                                    |                                                                     
tcatcaGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCa                                                                     >  1:5208177/1‑71 (MQ=255)
  atcaGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                                    <  1:739018/70‑1 (MQ=255)
   tcaGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCt                                                                  <  1:2921582/71‑1 (MQ=255)
          gTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGAc                                                           <  1:1626945/71‑1 (MQ=255)
           tCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGAc                                                           <  1:5438625/70‑1 (MQ=255)
            tgATGCCATACAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCg                                                         >  1:4832129/2‑71 (MQ=255)
            cGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCg                                                         >  1:3647090/1‑71 (MQ=255)
             gATACCTTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCgg                                                        >  1:2364034/1‑71 (MQ=255)
             gATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCgg                                                        >  1:4304771/1‑71 (MQ=255)
               tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                                    >  1:5246443/1‑57 (MQ=255)
               tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                                    >  1:5135949/1‑57 (MQ=255)
               tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                                    >  1:2385760/1‑57 (MQ=255)
               tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                                    >  1:867204/1‑57 (MQ=255)
               tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGt                                                       >  1:652340/1‑70 (MQ=255)
               tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGt                                                       >  1:1882342/1‑70 (MQ=255)
               tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGACACGGCCATATGCAt                                                                    >  1:5125436/1‑57 (MQ=255)
                 ccatACAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATGTGGTAAACCGGTCAg                                                    <  1:3584754/68‑1 (MQ=255)
                 ccatACAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAg                                                    <  1:1652425/68‑1 (MQ=255)
                 ccGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAg                                                    <  1:4061678/71‑1 (MQ=255)
                 ccGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAg                                                    <  1:4882749/71‑1 (MQ=255)
                   gTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGaa                                                  >  1:1245798/1‑71 (MQ=255)
                    tACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGaa                                                  >  1:1790933/1‑70 (MQ=255)
                     aCAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCacg                                                >  1:2452247/1‑70 (MQ=255)
                     aCAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCa                                                                     <  1:3353916/50‑1 (MQ=255)
                      cAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggt                                                               >  1:1897407/1‑54 (MQ=16)
                      cAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggt                                                               >  1:2959397/1‑54 (MQ=16)
                      cAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggt                                                               >  1:2963213/1‑54 (MQ=16)
                      cAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggt                                                               >  1:2969872/1‑54 (MQ=16)
                      cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                                    >  1:2296876/1‑50 (MQ=255)
                      cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATc                                                                   >  1:3114443/1‑51 (MQ=255)
                      cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATc                                                                   >  1:2302745/1‑51 (MQ=255)
                      cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                                               >  1:3290189/1‑71 (MQ=255)
                      cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                                               >  1:2925148/1‑71 (MQ=255)
                      cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                                               >  1:4111320/1‑71 (MQ=255)
                        gcgcTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggta                                                              <  1:111725/54‑3 (MQ=12)
                         cgcTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggta                                                              <  1:1037542/53‑3 (MQ=12)
                         cgcTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggta                                                              <  1:4648563/53‑3 (MQ=12)
                         cgcTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggta                                                              <  1:1468219/53‑3 (MQ=12)
                         cgcAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                                               >  1:5112888/1‑68 (MQ=255)
                         cgcAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                                               >  1:1550717/1‑68 (MQ=255)
                          gctaCGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAg                                            <  1:2540851/67‑1 (MQ=255)
                          gctaCGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGa                                           <  1:3725503/68‑1 (MQ=255)
                            aaCGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGAtt                                         <  1:2322149/71‑1 (MQ=255)
                            aaCGCGACGGTAGTCACCGATGATACGGCCAAGGCCATATGCATCTGGAAGAc                                                           >  1:3947898/1‑53 (MQ=39)
                            aaCGCGACGGTAGTCACAGATGATACGGCCAAGGCCATATGCATCTGGCAGAc                                                           >  1:1878734/1‑53 (MQ=255)
                             aCGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGAtt                                         >  1:343396/1‑70 (MQ=255)
                              cgcgGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACGGGTCAGCACGCCAGAtt                                         <  1:2976377/69‑1 (MQ=255)
                              cgcgGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTa                                       >  1:1043154/1‑71 (MQ=255)
                              cgcgACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTa                                       <  1:3262171/71‑1 (MQ=255)
                              cgcgACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTa                                       >  1:1977826/1‑71 (MQ=255)
                              cgcgACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTa                                       <  1:4904901/71‑1 (MQ=255)
                                  aCGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGc                                   <  1:1586519/71‑1 (MQ=255)
                                      tAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACg                               >  1:3230450/1‑71 (MQ=255)
                                       aGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAac                                                 >  1:4555955/1‑52 (MQ=255)
                                       aGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAac                                                 >  1:4743364/1‑52 (MQ=255)
                                       aGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAac                                                 >  1:2650020/1‑52 (MQ=255)
                                        gTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACg                               >  1:1429881/1‑69 (MQ=255)
                                        gTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGAttt                                        <  1:1618357/60‑1 (MQ=255)
                                        gTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGAttt                                        <  1:267034/60‑1 (MQ=255)
                                         tCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCa                                             <  1:5566384/54‑1 (MQ=255)
                                         tCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCa                                             <  1:3137773/54‑1 (MQ=255)
                                           aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa                          >  1:5385352/1‑71 (MQ=255)
                                           aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa                          >  1:5506485/1‑71 (MQ=255)
                                           aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa                          >  1:1634714/1‑71 (MQ=255)
                                           aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa                          >  1:2137121/1‑71 (MQ=255)
                                           aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa                          >  1:3452840/1‑71 (MQ=255)
                                           aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa                          >  1:830147/1‑71 (MQ=255)
                                           aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa                          >  1:3952179/1‑71 (MQ=255)
                                           aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACAGGTCAGAACACCAGATTTACGGCAACGCAgg                           <  1:438047/70‑1 (MQ=255)
                                             cGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATg                        <  1:269486/71‑1 (MQ=255)
                                              gatgatACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTa                                       >  1:2434345/1‑55 (MQ=255)
                                              gatgatACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACg                                     >  1:2412064/1‑57 (MQ=255)
                                              gataatGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCAtat                       >  1:840490/1‑69 (MQ=255)
                                               atgatACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTc                      >  1:3351202/1‑71 (MQ=255)
                                               atgatACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTc                      >  1:417548/1‑71 (MQ=255)
                                                  atACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCg                    <  1:1230781/70‑1 (MQ=255)
                                                     cgcccacggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCAt                         >  1:291098/4‑62 (MQ=255)
                                                     cgcccacggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCAt                         >  1:2696991/4‑62 (MQ=255)
                                                        ccacggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGTCAACGCAGGATGTCCGGAGTGTa             <  1:4426013/71‑1 (MQ=255)
                                                        ccacggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTa             <  1:119365/71‑1 (MQ=255)
                                                        ccacggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTa             <  1:4890959/71‑1 (MQ=255)
                                                         cacggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTaa            <  1:609488/71‑1 (MQ=255)
                                                         cacggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTa             <  1:472761/70‑1 (MQ=255)
                                                         cacggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTaa            <  1:5234997/71‑1 (MQ=255)
                                                          acggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTaaa           >  1:1256356/1‑71 (MQ=255)
                                                          acggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTa             <  1:826443/69‑1 (MQ=255)
                                                          acggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTa             <  1:5222851/69‑1 (MQ=255)
                                                           cggccaTATGCATCTGGCAGACCTTTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTaaa           >  1:2340349/1‑70 (MQ=255)
                                                           cggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAAc          >  1:5312540/1‑71 (MQ=255)
                                                           cggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAAc          >  1:2896784/1‑71 (MQ=255)
                                                            ggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGc                              >  1:709788/1‑50 (MQ=255)
                                                            ggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAAca         <  1:5066423/71‑2 (MQ=255)
                                                             gccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAgc                           >  1:2408130/1‑51 (MQ=16)
                                                              ccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATc       <  1:4805222/71‑1 (MQ=255)
                                                               caTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCg      <  1:1392433/71‑1 (MQ=255)
                                                                 tatGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTa             <  1:2781513/62‑1 (MQ=255)
                                                                 tatGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGaa    <  1:4442888/71‑1 (MQ=255)
                                                                 tatGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGaa    <  1:1112119/71‑1 (MQ=255)
                                                                   tGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa                          >  1:1136120/1‑47 (MQ=255)
                                                                   tGCATCTGGCAGACCGGGCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAaca  >  1:3822322/1‑71 (MQ=255)
                                                                    |                                                                     
TCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACA  >  Exported/609671‑609808

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