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 R2 251 90.0 5200563 86.9% 4519289 59.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,314,255 T→C 9.1% H170H (CAT→CAC)  hisB → fused histidinol‑phosphatase and imidazoleglycerol‑phosphate dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,314,2550TC 9.1% 479.0 / 28.0 165H170H (CAT→CAC) hisBfused histidinol‑phosphatase and imidazoleglycerol‑phosphate dehydratase
Reads supporting (aligned to +/- strand):  ref base T (68/81);  new base C (9/6);  total (78/87)
Fisher's exact test for biased strand distribution p-value = 4.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

Only 100 of 165 total aligned reads displayed.

ACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAGGTGGCAGC  >  minE/1314188‑1314321
                                                                   |                                                                  
 cGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAg                                                                >  1:4897091/1‑71 (MQ=255)
 cGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAg                                                                >  1:1533311/1‑71 (MQ=255)
      gcgAAACCCTGAACTGGCCAATGATTGGCTAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCg                                                            >  1:1424555/1‑70 (MQ=255)
      gcgAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGt                                                           <  1:4373050/71‑1 (MQ=255)
      gcgAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGt                                                           <  1:2629900/71‑1 (MQ=255)
            cccTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATAcc                                                     <  1:832689/71‑1 (MQ=255)
            cccTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATAcc                                                     <  1:3515318/71‑1 (MQ=255)
             ccTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGt                                                           <  1:3337159/64‑1 (MQ=255)
             ccTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGt                                                           <  1:5039202/64‑1 (MQ=255)
             ccTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGt                                                           <  1:1899191/64‑1 (MQ=255)
             ccTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGt                                                           <  1:3089281/64‑1 (MQ=255)
             ccTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGt                                                           <  1:810835/64‑1 (MQ=255)
              cTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTa                                                                 >  1:4885427/1‑57 (MQ=255)
              cTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTa                                                                 >  1:4323976/1‑57 (MQ=255)
              cTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTa                                                                 >  1:267304/1‑57 (MQ=255)
                gAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCa                                                    >  1:3775269/1‑68 (MQ=255)
                 aaCTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACTCTCACGTAGTGCGTAATACCa                                                    <  1:1805889/67‑1 (MQ=255)
                 aaCTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCa                                                    <  1:2592339/67‑1 (MQ=255)
                 aaCTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCa                                                    <  1:314429/67‑1 (MQ=255)
                  aCTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCa                                                    <  1:3555971/66‑1 (MQ=255)
                   cTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAgaga                                              <  1:1984503/71‑1 (MQ=255)
                   cTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCaaa                                                  >  1:17229/1‑67 (MQ=255)
                   cTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCaaa                                                  >  1:2486804/1‑67 (MQ=255)
                   cTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCaaa                                                  >  1:4229983/1‑67 (MQ=255)
                   cTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCaaa                                                  >  1:2766331/1‑67 (MQ=255)
                    tGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGt                                                                  <  1:2463056/50‑1 (MQ=255)
                        cAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACg                                            >  1:5028104/1‑68 (MQ=255)
                        cAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACg                                            >  1:4603086/1‑68 (MQ=255)
                        cAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACg                                            >  1:1793442/1‑68 (MQ=255)
                        cAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACg                                            >  1:887210/1‑68 (MQ=255)
                        cAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACg                                            >  1:5008817/1‑68 (MQ=255)
                            gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGAtt                                      >  1:4574255/1‑70 (MQ=255)
                            gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGAtt                                      >  1:1585272/1‑70 (MQ=255)
                             aTTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTg                                     <  1:253287/70‑1 (MQ=255)
                             aTTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTg                                     <  1:4418471/70‑1 (MQ=255)
                             aTTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTg                                     <  1:1008812/70‑1 (MQ=255)
                             aTTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTg                                     <  1:1272825/70‑1 (MQ=255)
                             aTTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTg                                     <  1:4719074/70‑1 (MQ=255)
                             aTTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTg                                     <  1:1365159/70‑1 (MQ=255)
                               tGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACg                                  >  1:4176480/1‑71 (MQ=255)
                                ggCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAag                                                 >  1:1244201/1‑55 (MQ=255)
                                    aGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAaga                                                <  1:4117663/52‑1 (MQ=255)
                                    aGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAaga                                                <  1:5125765/52‑1 (MQ=255)
                                    aGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAaga                                                <  1:1766171/52‑1 (MQ=255)
                                    aGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGa                                    >  1:4266122/1‑64 (MQ=255)
                                    aGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGa                                    >  1:1851175/1‑64 (MQ=255)
                                     gCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAaga                                                <  1:1257516/51‑1 (MQ=255)
                                     gCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAgg                            <  1:1656102/71‑1 (MQ=255)
                                     gCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAgg                            <  1:2961535/71‑1 (MQ=255)
                                     gCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAgg                            <  1:2789752/71‑1 (MQ=255)
                                      cAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAgg                            <  1:2149265/70‑1 (MQ=255)
                                           cACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:320948/1‑71 (MQ=255)
                                           cACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:1790809/1‑71 (MQ=255)
                                           cACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:4959977/1‑71 (MQ=255)
                                           cACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:2889080/1‑71 (MQ=255)
                                           cACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:2113859/1‑71 (MQ=255)
                                           cACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:4773626/1‑71 (MQ=255)
                                            aCCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCt                     >  1:3225564/1‑71 (MQ=255)
                                            aCCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCt                     >  1:459884/1‑71 (MQ=255)
                                            aCCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCt                     >  1:443558/1‑71 (MQ=255)
                                            aCCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCt                     >  1:4341802/1‑71 (MQ=255)
                                              cAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTgg                   <  1:3747129/71‑1 (MQ=255)
                                              cAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTgg                   <  1:686964/71‑1 (MQ=255)
                                              cAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTg                    >  1:1914775/1‑70 (MQ=255)
                                                gACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      <  1:824663/66‑1 (MQ=255)
                                                gACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      <  1:2743391/66‑1 (MQ=255)
                                                gACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      <  1:1608998/66‑1 (MQ=255)
                                                gACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      <  1:3411827/66‑1 (MQ=255)
                                                    tGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTg             <  1:4081040/71‑1 (MQ=255)
                                                    tGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTg             <  1:2177690/71‑1 (MQ=255)
                                                    tGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTg             <  1:1863973/71‑1 (MQ=255)
                                                      aCCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGa            <  1:2819559/70‑1 (MQ=255)
                                                      aCCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGa            <  1:3264663/70‑1 (MQ=255)
                                                       ccGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATTGTGAAg          <  1:5349/71‑1 (MQ=255)
                                                       ccGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGa            <  1:5030434/69‑1 (MQ=255)
                                                       ccGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAg          <  1:4659851/71‑1 (MQ=255)
                                                       ccGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAg          <  1:1026924/71‑1 (MQ=255)
                                                       ccGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAg          <  1:1385081/71‑1 (MQ=255)
                                                       ccGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAg          <  1:2206856/71‑1 (MQ=255)
                                                       ccGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAg          <  1:2573922/71‑1 (MQ=255)
                                                         gTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:4015589/1‑57 (MQ=255)
                                                         gTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:2108208/1‑57 (MQ=255)
                                                         gTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:2327660/1‑57 (MQ=255)
                                                         gTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:2630871/1‑57 (MQ=255)
                                                         gTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:3267355/1‑57 (MQ=255)
                                                         gTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:3927542/1‑57 (MQ=255)
                                                         gTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:4673784/1‑57 (MQ=255)
                                                         gTTACGCTCATGTAGTGCGTAATACCAAAGAGAAGCACATTGa                                    >  1:2574003/1‑43 (MQ=255)
                                                         attACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      >  1:3934196/2‑57 (MQ=255)
                                                          ttACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGc                      <  1:4936718/56‑1 (MQ=255)
                                                          ttACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCg               <  1:1169022/63‑1 (MQ=255)
                                                          ttACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATCGACGTTCAGGTGTGGCTGGATCg               <  1:724097/63‑1 (MQ=255)
                                                             cGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAGGTgg      >  1:512816/1‑69 (MQ=255)
                                                               cTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAGGTGgcagc  <  1:4458385/71‑1 (MQ=255)
                                                               cTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAGGTGgcagc  <  1:1336521/71‑1 (MQ=255)
                                                               cTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAGGTGgcagc  <  1:1157994/71‑1 (MQ=255)
                                                                tCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAGGTGgcagc  >  1:3392973/1‑70 (MQ=255)
                                                                tCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAGGTGgcagc  >  1:3668002/1‑70 (MQ=255)
                                                                  aTGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAGGTGgcagc  >  1:3236493/1‑68 (MQ=255)
                                                                  aTGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAGGTGgcagc  >  1:3582306/1‑68 (MQ=255)
                                                                   |                                                                  
ACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCATGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTCAGGTGTGGCTGGATCGTGAAGGTGGCAGC  >  minE/1314188‑1314321

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