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 2,045,826 A→G 32.2% intergenic (+588/+207) yqiK → / ← rfaE conserved hypothetical protein/fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,045,8260AG32.2% 134.1 / 72.1 90intergenic (+588/+207)yqiK/rfaEconserved hypothetical protein/fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase
Reads supporting (aligned to +/- strand):  ref base A (24/37);  new base G (14/15);  total (38/52)
Fisher's exact test for biased strand distribution p-value = 4.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-01

Only 100 of 113 total aligned reads displayed.

TTGCGCGGGGTCCGGCGCTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAA  >  minE/2045756‑2045896
                                                                      |                                                                       
ttGCGCGGGGTCCGGCGCTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCgaa                                                                         <  1:4422296/71‑1 (MQ=255)
         gTCCGGCGCTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGcc                                                               >  1:4650558/1‑71 (MQ=255)
            cGGCGCTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCgaaga                                                                       >  1:4429500/1‑61 (MQ=255)
                gcTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGta                                                          >  1:5442407/1‑69 (MQ=255)
                    atcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGtat                                                         <  1:2333700/66‑1 (MQ=255)
                    atcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                     >  1:3343442/1‑70 (MQ=255)
                     tcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTg                                                            <  1:1552405/62‑1 (MQ=255)
                     tcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGaa                                                   <  1:2717963/71‑1 (MQ=255)
                       aacaaTCGGGGGGCAGCAAGGGGCTGAAACTGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGa                                                    <  1:892892/68‑1 (MQ=255)
                       aacaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCgaag                                                                        >  1:822613/1‑49 (MQ=255)
                       aacaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAg                                                 >  1:2466718/1‑71 (MQ=255)
                       aacaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAg                                                 >  1:5640262/1‑71 (MQ=255)
                        ctaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGaaa                                                  <  1:4132819/67‑1 (MQ=255)
                        acaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTg                                                            <  1:1271467/59‑1 (MQ=255)
                        acaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTg                                                            <  1:5090951/59‑1 (MQ=255)
                        acaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTg                                                            <  1:711585/59‑1 (MQ=255)
                               gggggCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCgaag                                                                        <  1:3182772/41‑1 (MQ=255)
                                  ggCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                     <  1:2562837/56‑1 (MQ=255)
                                  ggCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                     <  1:276982/56‑1 (MQ=255)
                                   gcagcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                     <  1:165441/55‑1 (MQ=255)
                                   gcagcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGa                                                    <  1:733399/56‑1 (MQ=255)
                                    cagcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAg‑g                                                                   >  1:2605999/1‑40 (MQ=40)
                                    cagcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAg                                    >  1:830053/1‑71 (MQ=255)
                                     agcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTa                                            <  1:4329956/62‑1 (MQ=255)
                                     agcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTa                                            <  1:2531398/62‑1 (MQ=255)
                                      gcaAGGGGCTGAAACGGGAAAGCCCCTCCCgaaga                                                                       <  1:4963063/35‑1 (MQ=40)
                                      gcaAGGGGCTGAAACGGGAAAGCCCCTCCCgaaga                                                                       <  1:3957118/35‑1 (MQ=40)
                                      gcaAGGGGCTGAAACGGGAAAGCCCCTCCCgaaga                                                                       <  1:4260276/35‑1 (MQ=40)
                                      gcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg                                                     <  1:4661619/52‑1 (MQ=255)
                                      gcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAgg                                                <  1:3000704/57‑1 (MQ=255)
                                      gcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTatg                                          >  1:4328361/1‑63 (MQ=255)
                                        aaGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGt                                              >  1:781119/1‑57 (MQ=255)
                                         aGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTa                                            >  1:3736880/1‑58 (MQ=255)
                                           gggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGTCCTTGTATAAGGAAAGGGTTa                                            <  1:1977594/56‑1 (MQ=255)
                                           acgCTGAAACGGGAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGt                               >  1:303292/3‑70 (MQ=0)
                                            ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGtat                                                         <  1:57129/42‑1 (MQ=255)
                                            ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtcat                            >  1:552372/1‑71 (MQ=255)
                                            ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtcat                            >  1:5627124/1‑71 (MQ=255)
                                            ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtcat                            >  1:3187602/1‑71 (MQ=255)
                                            cgCTGAAACGGGAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGtca                             <  1:1786500/70‑1 (MQ=1)
                                              cTGAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGaaa                                                  >  1:3653992/1‑47 (MQ=14)
                                              cTGAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatg                                          <  1:144998/55‑1 (MQ=14)
                                              cTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATaa                                                       >  1:442617/1‑42 (MQ=255)
                                                gAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGaa                                                   >  1:1492151/1‑44 (MQ=14)
                                                gAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACtcat                            >  1:1889915/1‑67 (MQ=14)
                                                gAAACGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACtcat                            >  1:1896669/1‑67 (MQ=14)
                                                gAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGtt                                             <  1:1190765/50‑1 (MQ=255)
                                                 aaaCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                        <  1:3787364/54‑1 (MQ=14)
                                                 aaaCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcatcg                       <  1:565443/71‑3 (MQ=11)
                                                 aaaCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATAc                       >  1:4899675/1‑71 (MQ=255)
                                                  aaCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAg                                    >  1:3535738/1‑57 (MQ=255)
                                                   aCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCAtgatga                                      >  1:3590871/1‑54 (MQ=14)
                                                   aCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCAtgatga                                      >  1:3633700/1‑54 (MQ=14)
                                                   aCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAATGAAAGGGTTATGATGAAGCTCGt                               <  1:5193989/61‑1 (MQ=255)
                                                      ggAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTCATCATCGTGgtg                  >  1:1155474/1‑70 (MQ=2)
                                                      ggAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgtt                  >  1:3793091/1‑71 (MQ=255)
                                                       gAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgt                   >  1:3680797/1‑70 (MQ=11)
                                                       gAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTCATCATCGTGgtgc                 >  1:3332284/1‑69 (MQ=2)
                                                       gAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttg                 <  1:2081641/71‑1 (MQ=255)
                                                        aaaGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTCATCATCGTGgtgc                 >  1:3132334/1‑68 (MQ=2)
                                                        aaaGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTCATCATCGTGgtgc                 >  1:4164927/1‑68 (MQ=2)
                                                          aGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGt                                              <  1:3505689/40‑1 (MQ=0)
                                                             cccTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACt                      <  1:1253870/60‑1 (MQ=255)
                                                              tcTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgtg                  <  1:3123410/63‑2 (MQ=11)
                                                              ccTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttgt           >  1:3907027/1‑70 (MQ=255)
                                                               cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtc                              <  1:3373786/50‑1 (MQ=255)
                                                               cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtc                              <  1:1663603/50‑1 (MQ=255)
                                                               cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTa         <  1:4919004/71‑1 (MQ=255)
                                                                tCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCat                                           <  1:128161/36‑1 (MQ=12)
                                                                tCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCat                                           <  1:1943990/36‑1 (MQ=12)
                                                                tCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCat                                           <  1:2965762/36‑1 (MQ=12)
                                                                 cccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCtac                                >  1:74665/1‑44 (MQ=9)
                                                                 cccGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATa                        >  1:4898656/1‑54 (MQ=255)
                                                                  ccGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTGgtga                 >  1:3161910/1‑59 (MQ=2)
                                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatga                                         >  1:4550644/1‑36 (MQ=12)
                                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatga                                         >  1:1660542/1‑36 (MQ=12)
                                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatga                                         >  1:5472944/1‑36 (MQ=12)
                                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                         <  1:3118384/52‑1 (MQ=9)
                                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                         <  1:3479904/52‑1 (MQ=9)
                                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                         <  1:213885/52‑1 (MQ=9)
                                                                  ccGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat                         <  1:2184869/52‑1 (MQ=9)
                                                                  ccGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttgt           <  1:2337461/66‑1 (MQ=255)
                                                                   cGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                        <  1:3931266/36‑1 (MQ=9)
                                                                   cGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                        <  1:2218638/36‑1 (MQ=9)
                                                                   cGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCatgat                                        <  1:3598393/36‑1 (MQ=9)
                                                                   cGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATa                        >  1:1020149/1‑52 (MQ=255)
                                                                   cGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTg                     <  1:2294832/55‑1 (MQ=255)
                                                                    gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATa                        >  1:525181/1‑51 (MQ=255)
                                                                    gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt    <  1:4698006/71‑1 (MQ=255)
                                                                    gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt    <  1:4307788/71‑1 (MQ=255)
                                                                    gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGt     >  1:5507266/1‑70 (MQ=255)
                                                                     aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgt                   >  1:1201610/1‑55 (MQ=255)
                                                                     aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt    >  1:3440667/1‑70 (MQ=255)
                                                                     aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTa   <  1:1849759/71‑1 (MQ=255)
                                                                     aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTa   <  1:2702621/71‑1 (MQ=255)
                                                                      agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTgg                    >  1:611677/1‑53 (MQ=255)
                                                                      agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTgg                    >  1:4303137/1‑53 (MQ=255)
                                                                      agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTgg                    >  1:3598080/1‑53 (MQ=255)
                                                                      agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTaa  <  1:1283014/71‑1 (MQ=255)
                                                                      agaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTaa  <  1:4262499/71‑1 (MQ=255)
                                                                      |                                                                       
TTGCGCGGGGTCCGGCGCTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAA  >  minE/2045756‑2045896

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