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
A5 F64 I1 R1 17 68.2 3417408 93.4% 3191859 100.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,338,928 C→A L107F (TTG→TTT)  mlaE ← ABC transporter maintaining OM lipid asymmetry, inner membrane permease protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,338,9280CA98.2% 191.4 / ‑3.7 54L107F (TTG→TTT) mlaEABC transporter maintaining OM lipid asymmetry, inner membrane permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (20/33);  total (20/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

CGGATCCACCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAACAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCACTATAAGTGGTCAGAACCAG  >  NC_000913/3338832‑3339023
                                                                                                |                                                                                               
cgatctcACCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAaaaaac                                                                                              <  2:995579/94‑1 (MQ=255)
cGGATCCACCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAaaaaac                                                                                              >  2:2436105/1‑100 (MQ=255)
   aTCCACCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAaaaaacaac                                                                                           >  2:1620070/1‑100 (MQ=255)
   aTCCACCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAaaaaacaac                                                                                           >  2:1946370/1‑100 (MQ=255)
     ccACCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAAcgc                                                                                         <  1:335958/100‑1 (MQ=255)
     ccACCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAAcgc                                                                                         <  2:335958/100‑1 (MQ=255)
       aCCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCgg                                                                                       >  2:1277/1‑100 (MQ=255)
       aCCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCgg                                                                                       >  1:1277/1‑100 (MQ=255)
       aCCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGACAAAAAACAACGCgg                                                                                       >  2:1513774/1‑100 (MQ=255)
           ccATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAac                                                                                   <  2:2322265/100‑1 (MQ=255)
              tcatcTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAaccac                                                                                >  1:191800/1‑100 (MQ=255)
              tcatcTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAaccac                                                                                >  2:191800/1‑100 (MQ=255)
               catcTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAaccacc                                                                               <  2:1850751/100‑1 (MQ=255)
                 tctcCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCgg                                                                             >  2:1522875/1‑100 (MQ=255)
                   tcCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACTAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGcc                                                                           >  2:1600974/1‑100 (MQ=255)
                    ccATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGccc                                                                          >  1:299151/1‑100 (MQ=255)
                    ccATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGccc                                                                          >  2:299151/1‑100 (MQ=255)
                     cATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGcccc                                                                         <  2:2479159/100‑1 (MQ=255)
                     cATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGcccc                                                                         >  2:1416055/1‑100 (MQ=255)
                           ggAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCa                                                                   >  2:1443205/1‑100 (MQ=255)
                            gagaGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCAc                                                                  <  2:2453557/100‑1 (MQ=255)
                              gagTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGc                                                                <  1:39618/100‑1 (MQ=255)
                              gagTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGc                                                                <  2:39618/100‑1 (MQ=255)
                               agTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCa                                                               <  2:99652/100‑1 (MQ=255)
                               agTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCa                                                               <  1:99652/100‑1 (MQ=255)
                                gTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAACAACAACGCGGCAACCACCGGCCCCAGTTCACGCAg                                                              <  2:1793213/100‑1 (MQ=255)
                                 ttGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCTGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGt                                                             <  2:1489075/100‑1 (MQ=255)
                                  tGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTa                                                            <  2:50859/100‑1 (MQ=255)
                                  tGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTa                                                            <  1:50859/100‑1 (MQ=255)
                                        gTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATa                                                      >  2:2512069/1‑100 (MQ=255)
                                                cATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGccacc                                              <  2:1980419/100‑1 (MQ=255)
                                                  tCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCTGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAg                                            <  1:195499/100‑1 (MQ=255)
                                                  tCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCTGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAg                                            <  2:195499/100‑1 (MQ=255)
                                                  tCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAg                                            <  2:1902084/100‑1 (MQ=255)
                                                       ccGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATAc                                       <  1:323304/100‑1 (MQ=255)
                                                       ccGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATAc                                       <  2:323304/100‑1 (MQ=255)
                                                         gATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATAccc                                     >  2:1367833/1‑100 (MQ=255)
                                                         gATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATAccc                                     <  2:1375531/100‑1 (MQ=255)
                                                             tCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGAc                                 <  2:631539/100‑1 (MQ=255)
                                                             tCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGAc                                 <  1:631539/100‑1 (MQ=255)
                                                              cTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACt                                >  2:1985181/1‑100 (MQ=255)
                                                                gCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTgg                              <  2:460482/100‑1 (MQ=255)
                                                                gCGGTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTgg                              <  1:460482/100‑1 (MQ=255)
                                                                  ggTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGtt                            >  2:1444837/1‑100 (MQ=255)
                                                                  ggTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGtt                            >  2:725248/1‑100 (MQ=255)
                                                                  ggTTAGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGtt                            >  1:725248/1‑100 (MQ=255)
                                                                      aGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCTCGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCg                        <  1:596740/100‑1 (MQ=255)
                                                                      aGCGCCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCTCGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCg                        <  2:596740/100‑1 (MQ=255)
                                                                       gcgcCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGc                       <  2:1566395/100‑1 (MQ=255)
                                                                        cgcCGAACCAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCa                      <  2:1247189/100‑1 (MQ=255)
                                                                               ccAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCACTATAAg               <  2:2430544/100‑1 (MQ=255)
                                                                               ccAGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCACTATAAg               >  2:2092891/1‑100 (MQ=255)
                                                                                 aGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCACTATAAGTg             <  1:424950/100‑1 (MQ=255)
                                                                                 aGCACGCCCGGCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCACTATAAGTg             <  2:424950/100‑1 (MQ=255)
                                                                                           gCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCACTATAAGTGGTCAGAACCa   <  1:501359/100‑1 (MQ=255)
                                                                                           gCAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCACTATAAGTGGTCAGAACCa   <  2:501359/100‑1 (MQ=255)
                                                                                            cAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCACTATAAGTGGTCAGAACCAg  >  1:709174/1‑100 (MQ=255)
                                                                                            cAAAAAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCACTATAAGTGGTCAGAACCAg  >  2:709174/1‑100 (MQ=255)
                                                                                                |                                                                                               
CGGATCCACCGCCATCATCTCCATACTGGAGAGTTGCTCTGTAGCGCGCATCAGGCCGATTTCTGCGGTTAGCGCCGAACCAGCACGCCCGGCAAACAACAACGCGGCAACCACCGGCCCCAGTTCACGCAGTAGCGATAACGCCACCAGCATACCCAGACTGGTTTCCGCACTATAAGTGGTCAGAACCAG  >  NC_000913/3338832‑3339023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A