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 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 minE 1,837,465 A→G 27.7% H318H (CAT→CAC)  nlpD ← predicted outer membrane lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,837,4650AG27.7% 151.2 / 70.0 106H318H (CAT→CAC) nlpDpredicted outer membrane lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (36/40);  new base G (17/12);  total (54/52)
Fisher's exact test for biased strand distribution p-value = 3.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.90e-01

Only 100 of 110 total aligned reads displayed.

CCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCT  >  minE/1837395‑1837531
                                                                      |                                                                  
ccTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTa                                                                    >  1:1506986/1‑71 (MQ=255)
 cTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTAt                                                                   >  1:3004534/1‑71 (MQ=255)
    aaCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt                                                                 >  1:3185901/1‑70 (MQ=255)
     aCTTCTTGTTGTTCCCGGACCAGGATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt                                                               <  1:2500831/71‑1 (MQ=255)
     aCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt                                                               <  1:2222326/71‑1 (MQ=255)
     aCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt                                                               <  1:5127570/71‑1 (MQ=255)
     aCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt                                                               <  1:3627885/71‑1 (MQ=255)
     aCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGtt                                                                <  1:877407/70‑1 (MQ=255)
      cttcttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGtt                                                                <  1:3885381/69‑1 (MQ=255)
      cttcttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGtt                                                                <  1:254132/69‑1 (MQ=255)
      cttcttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGtt                                                                <  1:2011674/69‑1 (MQ=255)
            gttgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgatga                                                          <  1:4754187/69‑1 (MQ=255)
            gttgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgatga                                                          <  1:5424680/69‑1 (MQ=255)
            gttgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTgatgat                                                         <  1:4205122/70‑1 (MQ=255)
             ttgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATa                                                        <  1:343340/70‑1 (MQ=255)
               gttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgat                                                            >  1:3393886/1‑64 (MQ=255)
                ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATc                                                     <  1:470958/70‑1 (MQ=255)
                ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATc                                                     <  1:1129091/70‑1 (MQ=255)
                ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa                                                    <  1:4905618/71‑1 (MQ=255)
                  cccGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGtt                                                                >  1:2303730/1‑57 (MQ=255)
                    tttaCCAGCATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGAt                                                 <  1:940574/67‑1 (MQ=255)
                    tttaCCAGCATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGAt                                                 <  1:216349/67‑1 (MQ=255)
                         cAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTAt                                                                   <  1:918072/47‑1 (MQ=255)
                         cAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGt                                           <  1:210467/71‑1 (MQ=255)
                          aGCATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGt                                           <  1:2273518/70‑1 (MQ=255)
                           gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt                                                                 >  1:4418962/1‑47 (MQ=255)
                           gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt                                                                 >  1:3298963/1‑47 (MQ=255)
                           gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt                                                                 >  1:1609507/1‑47 (MQ=255)
                           gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTgatgat                                                         <  1:760127/55‑1 (MQ=255)
                           gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTgatgat                                                         <  1:3767932/55‑1 (MQ=255)
                           gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTgatgat                                                         <  1:5178212/55‑1 (MQ=255)
                           gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAg                                         <  1:4288213/71‑1 (MQ=255)
                           gCATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAg                                         >  1:4278880/1‑71 (MQ=255)
                            cATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGc                                        <  1:169398/71‑1 (MQ=255)
                            cATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGc                                        >  1:5110646/1‑71 (MQ=255)
                             atcgtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGc                                        >  1:2584178/4‑70 (MQ=255)
                              ttGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTa                                                                    <  1:4052296/41‑1 (MQ=255)
                              ttGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTa                                                                    <  1:398584/41‑1 (MQ=255)
                              ttGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCg                                            >  1:2007803/1‑65 (MQ=255)
                              ttGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAg                                         >  1:1663468/1‑68 (MQ=255)
                              ttGTGTAGTTATGGGCGTAGGCACTCAGGTAATCATCATTa                                                                    <  1:503388/41‑1 (MQ=255)
                               tgtgTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCcgc                                     >  1:4724543/1‑71 (MQ=255)
                               tgtgTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCcg                                      >  1:4044360/1‑70 (MQ=255)
                               tgtgTCGTTATGGGAGTAGGCACTCATGTAATCATCATTATGTTTGATGATAATCATATTAACg                                            >  1:5221032/1‑64 (MQ=255)
                                gtgtCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCcgcg                                    >  1:1290134/1‑71 (MQ=255)
                                gtgtCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCcgcg                                    >  1:3937281/1‑71 (MQ=255)
                                gtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCcacg                                    >  1:3550347/1‑71 (MQ=255)
                                gtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCcacg                                    >  1:865233/1‑71 (MQ=255)
                                gtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACAGTAGCcacg                                    >  1:5366931/1‑71 (MQ=255)
                                 tgtCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt                                                               <  1:4988662/43‑1 (MQ=255)
                                 tgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATgaga                                                  >  1:3683978/1‑56 (MQ=255)
                                 tgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATgaga                                                  >  1:744114/1‑56 (MQ=255)
                                   tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAg                                         >  1:832223/4‑63 (MQ=255)
                                   tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCa                                  <  1:4151842/67‑1 (MQ=255)
                                   tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCa                                  <  1:147037/67‑1 (MQ=255)
                                   tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAg                                 >  1:4552884/4‑71 (MQ=255)
                                   tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAg                                 >  1:435145/4‑71 (MQ=255)
                                   tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtga                                                             >  1:5143050/1‑43 (MQ=255)
                                   tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAg                                                   <  1:5070809/53‑1 (MQ=255)
                                    cattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTAcc                                             >  1:1162839/3‑58 (MQ=255)
                                    cattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAg                                 >  1:5488917/3‑70 (MQ=255)
                                     gTTATGGGCGTAGGCACTCAGGTAATCATCATTAt                                                                   <  1:2391443/35‑1 (MQ=255)
                                     gTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAgcg                               >  1:279509/1‑71 (MQ=255)
                                     gTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAgcg                               >  1:171463/1‑71 (MQ=255)
                                     gTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAga                                >  1:2485721/1‑69 (MQ=255)
                                     attATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGAt                                                 >  1:2727593/2‑53 (MQ=255)
                                     attATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTAcc                                             >  1:3314409/2‑57 (MQ=255)
                                     attATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGccac                                     <  1:2958374/64‑3 (MQ=255)
                                     attATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgct                               <  1:4579251/70‑2 (MQ=255)
                                      ttATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgctg                              <  1:2302439/71‑3 (MQ=255)
                                      ttATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgctg                              <  1:5610259/71‑3 (MQ=255)
                                      ttATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgctg                              <  1:4749363/71‑3 (MQ=255)
                                      taaTGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCa                                  <  1:1184967/65‑1 (MQ=255)
                                       tATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAgcgc                              >  1:4100491/1‑70 (MQ=255)
                                         tGGGCGTAGGCACTCAGGTAATCATCATTTTGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGt                            >  1:1414191/1‑70 (MQ=255)
                                         tGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGtt                           <  1:2870711/71‑1 (MQ=255)
                                          gggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATaa                                                       >  1:3229625/1‑42 (MQ=255)
                                          gggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAAt                                                      >  1:4626672/1‑43 (MQ=255)
                                          gggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAAt                                                      >  1:4294273/1‑43 (MQ=255)
                                            gCGTAGGCACTCAGGTAATCATCATTATGTTTgatgat                                                         <  1:1852372/38‑1 (MQ=255)
                                               tAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa                                                    <  1:1068833/40‑1 (MQ=255)
                                                 ggCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCa                    >  1:2287529/1‑70 (MQ=255)
                                                  gCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATa                  <  1:1831448/71‑1 (MQ=255)
                                                     cTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTAcc                        <  1:4423282/62‑1 (MQ=255)
                                                     cTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaac               <  1:2100593/71‑1 (MQ=255)
                                                       cAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaa             >  1:4076349/1‑71 (MQ=255)
                                                         ggTAATCATCATTATGTTTGATGATAATCAGATTACCGTAg                                         <  1:1838597/41‑1 (MQ=255)
                                                         ggTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAAcg           >  1:1033989/1‑71 (MQ=255)
                                                          gTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATa                  <  1:893411/63‑1 (MQ=255)
                                                            aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaac               >  1:2230364/1‑64 (MQ=255)
                                                            aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaac               >  1:5385861/1‑64 (MQ=255)
                                                            aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaac               >  1:775615/1‑64 (MQ=255)
                                                               catcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAg                                 >  1:2394416/1‑43 (MQ=255)
                                                               catcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAg                                 >  1:3969487/1‑43 (MQ=255)
                                                               catcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAg                                 >  1:3919408/1‑43 (MQ=255)
                                                               catcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaac               <  1:1029486/61‑1 (MQ=255)
                                                                atcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaa             >  1:2835029/1‑62 (MQ=255)
                                                                atcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCAt    <  1:43273/71‑1 (MQ=255)
                                                                   atTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCt  <  1:5115252/70‑1 (MQ=255)
                                                                    ttATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATaaa                >  1:4966377/1‑55 (MQ=255)
                                                                      |                                                                  
CCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCT  >  minE/1837395‑1837531

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A