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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,980,009 T→C 13.3% intergenic (‑6/+19) mdtF ← / ← mdtE multidrug transporter, RpoS‑dependent/multidrug resistance efflux transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,980,0090TC13.3% 152.2 / 15.7 60intergenic (‑6/+19)mdtF/mdtEmultidrug transporter, RpoS‑dependent/multidrug resistance efflux transporter
Reads supporting (aligned to +/- strand):  ref base T (28/24);  new base C (2/6);  total (30/30)
Fisher's exact test for biased strand distribution p-value = 2.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.60e-01

CAAGCATCATAATAATGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTGGAGGAAATTGCT  >  W3110S.gb/3979940‑3980076
                                                                     |                                                                   
cAAGCATCATAATAATGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTc                                                                    <  1:2150469/71‑1 (MQ=255)
       catAATAATGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCtt                                                               >  1:638965/1‑69 (MQ=255)
       catAATAATGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCtt                                                               >  1:4299707/1‑69 (MQ=255)
       catAATAATGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAAAAGTTAGCCATGAAAGTCCCCtt                                                               >  1:3238347/1‑69 (MQ=255)
          aataatGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTcc                                                                   <  1:2995218/62‑1 (MQ=255)
             aatGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCt                                                         >  1:5072719/1‑69 (MQ=255)
             aatGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTg                                                        >  1:2473379/1‑70 (MQ=255)
             aatGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTg                                                        >  1:171441/1‑70 (MQ=255)
              atGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGc                                                       >  1:1839594/1‑70 (MQ=255)
              atGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGc                                                       <  1:740964/70‑1 (MQ=255)
                       aCCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGCCCCCTTAAGCCTGCAACGTTATTg                                             >  1:3217358/1‑71 (MQ=255)
                         ccAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGtt                                           <  1:3556482/71‑1 (MQ=255)
                          cAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGCCCCCTTAAGCCTGCAACGTTATTGttt                                          >  1:565950/1‑71 (MQ=255)
                           aGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTc                                         <  1:3433852/71‑1 (MQ=255)
                            ggCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTAt                                               >  1:1395111/1‑64 (MQ=255)
                             gCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCtt                                                               <  1:3492306/47‑1 (MQ=255)
                             gCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGc                                                           >  1:3803582/1‑51 (MQ=255)
                             gCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTc                                         <  1:2592681/69‑1 (MQ=255)
                             gCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCg                                        >  1:1166661/1‑70 (MQ=255)
                             gCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGa                                       <  1:4703051/71‑1 (MQ=255)
                               aaaaaCCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGtt                                                 >  1:4451909/1‑59 (MQ=255)
                                  aaCCGGGCGATCAATAAAATAGTTAGCCATGAAAGTcccc                                                                 >  1:4844986/1‑40 (MQ=255)
                                  aaCCGGGCGATCAATAAAATAGTTAGCCATGAAAGTcccc                                                                 >  1:4677889/1‑40 (MQ=255)
                                        gCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGtt                                           <  1:2793644/56‑1 (MQ=255)
                                        gCGATCAATAAAATAGTTAGCCATGAAAGCCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTgg                            <  1:5088410/71‑1 (MQ=255)
                                        gCGATCAATAAAATAGTTAGCCATGAAAGCCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTgg                            <  1:4621369/71‑1 (MQ=255)
                                        gCGATCAATAAAATAGTTAGCCAAGAAAGCCCCCTTAAGCCTGCAACGTTAtt                                              <  1:827291/53‑1 (MQ=255)
                                          gATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCg                          <  1:3431137/71‑1 (MQ=255)
                                           aTCAATAAAATAGTTAGCCATGAAAGTCCCGTTAAGCCTGCAACGTTATTGTTTCGATTc                                    <  1:959448/60‑1 (MQ=255)
                                           aTCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTAt                                               >  1:251659/1‑49 (MQ=255)
                                            tCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCaa                                                     >  1:1853605/1‑42 (MQ=255)
                                            tCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTTTTTc                                         <  1:1897090/54‑1 (MQ=255)
                                            tCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCgg                                  <  1:601971/61‑1 (MQ=255)
                                            tCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGtt                        <  1:4982870/71‑1 (MQ=255)
                                              aaTAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGAt                                      <  1:1141305/55‑1 (MQ=255)
                                              aaTAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGtttt                      <  1:2059436/71‑1 (MQ=255)
                                                tAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTAtt                                              <  1:2226045/45‑1 (MQ=255)
                                                tAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTc                     >  1:759909/1‑70 (MQ=255)
                                                 aaaaTAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCct                   >  1:535926/1‑71 (MQ=255)
                                                  aaaTAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGc                               >  1:3253018/1‑58 (MQ=255)
                                                  aaaTAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCctg                  >  1:4601634/1‑71 (MQ=255)
                                                   aaTAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCctg                  <  1:361387/70‑1 (MQ=255)
                                                        ttAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGttt                       <  1:4620623/60‑1 (MQ=255)
                                                         tAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTggag           >  1:2364640/1‑71 (MQ=255)
                                                          aGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTg                                             >  1:5048983/1‑36 (MQ=255)
                                                          aGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTggag           >  1:190346/1‑70 (MQ=255)
                                                           gCCATGAAAGCCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTggagga         <  1:4773598/71‑1 (MQ=255)
                                                             cATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTGGAGGaaa       <  1:3677430/71‑1 (MQ=255)
                                                             cATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTGGAGGaaa       <  1:3187295/71‑1 (MQ=255)
                                                              aTGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCt                              >  1:367362/1‑47 (MQ=255)
                                                              aTGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTGGAGGAAAt      >  1:4892828/1‑71 (MQ=255)
                                                               tGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTc                                    <  1:4452387/40‑1 (MQ=255)
                                                               tGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGc                               <  1:2680473/45‑1 (MQ=255)
                                                               tGAAAGCCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCctggctgg             <  1:1763979/63‑1 (MQ=255)
                                                               tGAAAGCCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTGGAGGAAAtt     <  1:4598603/71‑1 (MQ=255)
                                                                gAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGtt                        >  1:2192719/1‑51 (MQ=255)
                                                                gAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGtt                        >  1:2683411/1‑51 (MQ=255)
                                                                 aaaGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGt                                 >  1:2979112/1‑41 (MQ=255)
                                                                 aaaGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTg                             >  1:2427484/1‑45 (MQ=255)
                                                                  aaGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTGGAGGAAATTGCt  <  1:4181544/71‑1 (MQ=255)
                                                                     tCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCctggctgg             <  1:2185322/57‑1 (MQ=255)
                                                                     |                                                                   
CAAGCATCATAATAATGGCAAGTACCCAGGCAAAAACCGGGCGATCAATAAAATAGTTAGCCATGAAAGTCCCCTTAAGCCTGCAACGTTATTGTTTCGATTCGGTGCTGGCGTTTTCCTGGCTGGAGGAAATTGCT  >  W3110S.gb/3979940‑3980076

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