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
A14 F1 I2 R1 70 59.9 2639336 94.5% 2494172 113.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,271,600 (C)5→6 coding (171/1146 nt) garK ← glycerate kinase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,271,5951.C98.3% 218.3 / ‑3.6 59coding (176/1146 nt)garKglycerate kinase I
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (27/31);  total (27/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TCGCGTTTTTCCGCAGGTACCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAG‑C‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCG  >  NC_000913/3271457‑3271720
                                                                                                                                           |                                                                                                                              
tCGCGTTTTTCCGCAGGTACCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAg                                                                                                                                 <  2:1060244/139‑1 (MQ=255)
           cGCAGGTACCAGCTCCAGCCCACTGGCCGCCGCCATTTCAACAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGt                                                                                                                     <  1:788363/139‑1 (MQ=255)
              aGGTACCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGc                                                                                                                  <  2:943622/139‑1 (MQ=255)
                  aCCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCa                                                                                                              >  2:1254622/1‑139 (MQ=255)
                          cAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGt                                                                                                                     >  1:790088/1‑124 (MQ=255)
                          cAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGt                                                                                                                     <  2:790088/124‑1 (MQ=255)
                          cAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGc                                                                                                      <  2:529208/139‑1 (MQ=255)
                          cAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGc                                                                                                      >  1:1097254/1‑139 (MQ=255)
                          cAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGc                                                                                                      >  2:302750/1‑139 (MQ=255)
                          cAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGc                                                                                                      >  1:1075375/1‑139 (MQ=255)
                          cAGCCCACTGGCCACCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGc                                                                                                      >  1:1202981/1‑139 (MQ=255)
                           aGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAatc                                                                                                           >  2:475033/1‑133 (MQ=255)
                           aGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAatc                                                                                                           <  1:475033/133‑1 (MQ=255)
                            gCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCtt                                                                                                    >  1:876686/1‑139 (MQ=255)
                             cccACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCGTc                                                                                                   <  1:1254622/139‑1 (MQ=255)
                                    tccgccgccATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGt                                                                                                                     >  1:823106/2‑114 (MQ=255)
                                    gccgccgccATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGATGTTCAGCC‑CCCCTGGGt                                                                                                                     <  2:823106/114‑1 (MQ=255)
                                        ccgccATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCtt                                                                                        <  2:1135146/139‑1 (MQ=255)
                                                   aTAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCg                                                                             >  2:499912/1‑139 (MQ=255)
                                                        cgcgGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAAc                                                                        <  2:340220/139‑1 (MQ=255)
                                                           ggTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCgg                                                                     <  1:1172464/139‑1 (MQ=255)
                                                             ttttGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa                                                                   <  1:564265/139‑1 (MQ=255)
                                                             ttttGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa                                                                   <  2:1263146/139‑1 (MQ=255)
                                                             ttttGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa                                                                   <  1:499912/139‑1 (MQ=255)
                                                                  ccATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGaa                                                              <  2:1271939/139‑1 (MQ=255)
                                                                    aTCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAAc                                                            <  2:509306/139‑1 (MQ=255)
                                                                       gCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTa                                                         >  1:720778/1‑139 (MQ=255)
                                                                         cGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAG‑CGCCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACt                                                       <  1:755440/139‑1 (MQ=255)
                                                                                cccccAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACg                                                           <  1:1224013/128‑1 (MQ=255)
                                                                                cccccAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACg                                                           >  2:1224013/1‑128 (MQ=255)
                                                                                 ccccAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCa                                               >  2:696418/1‑139 (MQ=255)
                                                                                      aCTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAAcc                                                                       <  2:660132/110‑1 (MQ=255)
                                                                                      aCTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAAcc                                                                       >  1:660132/1‑110 (MQ=255)
                                                                                         ggCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAAt                                       <  1:302750/139‑1 (MQ=255)
                                                                                         ggCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAAt                                       <  2:876686/139‑1 (MQ=255)
                                                                                          gCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa                                                                   >  1:287508/1‑110 (MQ=255)
                                                                                          gCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa                                                                   <  2:287508/110‑1 (MQ=255)
                                                                                          gCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAAtt                                      >  2:414825/1‑139 (MQ=255)
                                                                                          gCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAAtt                                      >  1:492729/1‑139 (MQ=255)
                                                                                          gCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAAtt                                      >  2:1292129/1‑139 (MQ=255)
                                                                                                aCTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGa                                <  2:1097254/139‑1 (MQ=255)
                                                                                                  tttCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGaaa                              >  1:229613/1‑139 (MQ=255)
                                                                                                   ttCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAAt                             <  1:461493/139‑1 (MQ=255)
                                                                                                       cGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCtt                         <  1:1153075/139‑1 (MQ=255)
                                                                                                       cGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCtt                         <  2:492729/139‑1 (MQ=255)
                                                                                                        gCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCAcc                                                                                               <  2:1027750/68‑1 (MQ=255)
                                                                                                        gCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCAcc                                                                                               >  1:1027750/1‑68 (MQ=255)
                                                                                                            aGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTc                                                                                           >  2:1086253/1‑68 (MQ=255)
                                                                                                            aGCGGCCCTGTAACCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTc                                                                                           <  1:1086253/68‑1 (MQ=255)
                                                                                                                        aCCCAGGCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCa        <  2:187355/139‑1 (MQ=255)
                                                                                                                             ggCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAAc                                                                        >  2:266315/1‑70 (MQ=255)
                                                                                                                             ggCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAAc                                                                        <  1:266315/70‑1 (MQ=255)
                                                                                                                              gCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGt                                                                                             <  2:323848/48‑1 (MQ=38)
                                                                                                                              gCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGt                                                                                             >  1:323848/1‑48 (MQ=38)
                                                                                                                              gCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCg  >  1:163836/1‑139 (MQ=255)
                                                                                                                              gCGTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCg  >  1:1062333/1‑139 (MQ=255)
                                                                                                                                gTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAAt                             <  1:630794/110‑1 (MQ=255)
                                                                                                                                gTGACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAAt                             >  2:630794/1‑110 (MQ=255)
                                                                                                                                  gACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGaa                               <  2:328103/106‑1 (MQ=255)
                                                                                                                                  gACGTTCAGCC‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGaa                               >  1:328103/1‑106 (MQ=255)
                                                                                                                                           |                                                                                                                              
TCGCGTTTTTCCGCAGGTACCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAG‑C‑CCCCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCG  >  NC_000913/3271457‑3271720

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A