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 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,359,876 C→T 30.1% noncoding (1219/2905 nt) rrlA ← 23S ribosomal RNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,359,8760CT30.1% 175.2 / 87.2 107noncoding (1219/2905 nt)rrlA23S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base C (45/29);  new base T (17/15);  total (62/45)
Fisher's exact test for biased strand distribution p-value = 5.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.26e-01

Only 100 of 107 total aligned reads displayed.

CCCGCTTTATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCG  >  minE/2359815‑2359942
                                                             |                                                                  
cccGCTTTATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTca                                                           >  1:3244392/1‑71 (MQ=31)
 ccGCTTTATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTca                                                           >  1:2072260/1‑70 (MQ=255)
     tttATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGc                                                      >  1:620104/1‑71 (MQ=34)
       tATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCt                                                     <  1:3209900/70‑1 (MQ=35)
       tATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCt                                                     <  1:1920791/70‑1 (MQ=255)
         tCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:3318852/1‑63 (MQ=33)
         tCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:3619005/1‑63 (MQ=33)
         tCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:270549/1‑63 (MQ=33)
         tCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:656596/1‑63 (MQ=33)
         tCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:3538060/1‑63 (MQ=33)
         tCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:2677386/1‑63 (MQ=33)
         tCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:1213155/1‑63 (MQ=33)
         tCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:333500/1‑63 (MQ=33)
            ttACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGa                                               <  1:758498/71‑1 (MQ=34)
            ttACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGa                                               <  1:3508397/71‑1 (MQ=34)
            ttACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGa                                               <  1:1878149/71‑1 (MQ=34)
            ttACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACa                                                 >  1:3284138/1‑69 (MQ=255)
              aCTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGaa                                              <  1:1113267/70‑1 (MQ=35)
                 tATGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCt                                          >  1:1733412/1‑71 (MQ=255)
                 tATGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCt                                          >  1:816955/1‑71 (MQ=255)
                 tATGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCt                                          >  1:286212/1‑71 (MQ=255)
                  aTGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGc                                           <  1:2500407/69‑1 (MQ=35)
                  aTGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGc                                           <  1:799708/69‑1 (MQ=255)
                  aTGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGc                                           <  1:2712408/69‑1 (MQ=255)
                  aTGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGc                                           <  1:147476/69‑1 (MQ=255)
                  aTGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTc                                         >  1:2532976/1‑71 (MQ=255)
                  aTGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTc                                         >  1:1464411/1‑71 (MQ=255)
                   tGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTcc                                        <  1:1498531/71‑1 (MQ=34)
                   tGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTcc                                        >  1:1789306/1‑71 (MQ=255)
                   tGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTcc                                        >  1:596053/1‑71 (MQ=255)
                     tCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTcccc                                      >  1:905465/1‑71 (MQ=255)
                      cAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTccc                                       >  1:554244/1‑69 (MQ=35)
                       aGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTa                                    >  1:38793/1‑71 (MQ=34)
                       aGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCt                                     <  1:3086873/70‑1 (MQ=255)
                        gCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTAc                                   >  1:2665708/1‑71 (MQ=34)
                        gCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTAc                                   >  1:2849505/1‑71 (MQ=34)
                        gCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTAc                                   >  1:2855163/1‑71 (MQ=34)
                        gCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTcaca                                                         <  1:1847775/49‑1 (MQ=11)
                        gCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTcaca                                                         <  1:2857237/49‑1 (MQ=11)
                        gCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTcaca                                                         <  1:3619016/49‑1 (MQ=11)
                        gCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAgg                                                       <  1:2865502/51‑1 (MQ=11)
                         cATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcaca                                                         >  1:3619066/1‑48 (MQ=38)
                          aTTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTAccc                                 <  1:1902429/71‑1 (MQ=34)
                          aTTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAgg                                                       >  1:150393/1‑49 (MQ=11)
                           ttCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGaa                                              <  1:258678/57‑1 (MQ=35)
                             cGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:3135844/1‑43 (MQ=35)
                             cGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:3155009/1‑43 (MQ=35)
                             cGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:3417643/1‑43 (MQ=35)
                             cGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTcac                                                          >  1:38989/1‑43 (MQ=35)
                             cGCACTTCTGATACCTCCAGCATGACTCACAGCACACCTTcac                                                          >  1:1184585/1‑43 (MQ=255)
                              gCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTACCcaaca                             <  1:1275175/71‑1 (MQ=255)
                              gCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTACCcaaca                             <  1:3680372/71‑1 (MQ=255)
                               cACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCcaacaa                            >  1:2317094/1‑71 (MQ=34)
                               cACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCcaacaa                            >  1:2171682/1‑71 (MQ=34)
                                  ttCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAacaaca                          >  1:1931448/1‑70 (MQ=37)
                                    cTGATACCTCCAGCATACCTCACAGTACACCTTca                                                           >  1:2978745/1‑35 (MQ=11)
                                    cTGATACCTCCAGCATACCTCACAGTACACCTTca                                                           >  1:1584788/1‑35 (MQ=11)
                                          ccTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAg                                                <  1:3156195/40‑1 (MQ=40)
                                          ccTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAgtgt                  <  1:2956426/70‑1 (MQ=255)
                                          ccTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAgtgt                  <  1:327005/70‑1 (MQ=255)
                                            tCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTACCca                                <  1:2146850/54‑1 (MQ=11)
                                            tCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTACCca                                <  1:2022942/54‑1 (MQ=11)
                                             ccAGCATACCTCACAGTACACCTTCACAGGCTTACAGaa                                              >  1:3600581/1‑39 (MQ=14)
                                              cAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCt              <  1:3538609/70‑1 (MQ=255)
                                              cAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCt              <  1:1153496/70‑1 (MQ=255)
                                               aGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCca                                >  1:2651308/1‑51 (MQ=35)
                                               aGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTg             >  1:643019/1‑70 (MQ=255)
                                               aGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTg             >  1:1843306/1‑70 (MQ=255)
                                               aGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGc            >  1:815473/1‑71 (MQ=255)
                                               aGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGc            >  1:1684763/1‑71 (MQ=255)
                                               aGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTa                                    >  1:940086/1‑47 (MQ=11)
                                               aGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTa                                    >  1:3007129/1‑47 (MQ=11)
                                               aGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTa                                    >  1:2688267/1‑47 (MQ=11)
                                                gCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGcc           <  1:2597239/71‑1 (MQ=255)
                                                gCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGcc           <  1:1707490/71‑1 (MQ=255)
                                                  aTGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCcaac                              >  1:1930489/1‑50 (MQ=38)
                                                  aTGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCcaac                              >  1:56829/1‑50 (MQ=38)
                                                  aTGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCcaac                              >  1:1817645/1‑50 (MQ=38)
                                                  aTGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGc         <  1:3717492/71‑1 (MQ=255)
                                                      cTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCcaacaa                            >  1:901741/1‑48 (MQ=38)
                                                      cTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCt     >  1:2088853/1‑71 (MQ=255)
                                                       tCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCtt    >  1:2272935/1‑71 (MQ=255)
                                                        cacaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATa                      <  1:2212821/52‑1 (MQ=255)
                                                        cacaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATa                      <  1:2434110/52‑1 (MQ=255)
                                                        cacaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATa                      <  1:2702086/52‑1 (MQ=255)
                                                        cacaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATa                      <  1:137120/52‑1 (MQ=255)
                                                        cacaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTc   >  1:2203743/1‑71 (MQ=255)
                                                        cacaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTc   >  1:3241703/1‑71 (MQ=255)
                                                        cacaGAACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATa                      <  1:2443179/52‑1 (MQ=255)
                                                         acaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCg  <  1:3022421/71‑1 (MQ=255)
                                                         acaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCg  <  1:1260261/71‑1 (MQ=255)
                                                         acaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCg  <  1:1340706/71‑1 (MQ=255)
                                                         acaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCg  <  1:1355087/71‑1 (MQ=255)
                                                         acaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCg  <  1:781356/71‑1 (MQ=255)
                                                         acaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCg  <  1:1362686/71‑1 (MQ=255)
                                                         acaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCg  >  1:271267/1‑71 (MQ=255)
                                                         acaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCg  >  1:2359290/1‑71 (MQ=255)
                                                         acaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCg  <  1:3150898/71‑1 (MQ=255)
                                                         acaGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCg  >  1:2193247/1‑71 (MQ=255)
                                                           aGCACACCTTCACAGGCTTACAGAACGCTCCCCTa                                    >  1:140468/1‑35 (MQ=40)
                                                             |                                                                  
CCCGCTTTATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCTTCG  >  minE/2359815‑2359942

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A