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
A1 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,633,778 T→C 14.1% C97C (TGT→TGC)  yigG → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,633,7780TC14.1% 181.0 / 20.8 78C97C (TGT→TGC) yigGpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (29/37);  new base C (3/7);  total (32/46)
Fisher's exact test for biased strand distribution p-value = 5.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.42e-01

CTTATGTTTTTGGTACATTAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCTTG  >  W3110S.gb/3633708‑3633842
                                                                      |                                                                
cTTATGTTTTTGGTACATTAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGt                                                                  <  1:1213955/71‑1 (MQ=255)
    tGTTTTTGGTACATTAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCa                                                               <  1:4289566/70‑1 (MQ=255)
        tttGGTACATTAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGAACAGGCa                                                           <  1:1479457/70‑1 (MQ=255)
         ttGGTACATTAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGAACAGGCa                                                           <  1:3387666/69‑1 (MQ=255)
            gTACATTAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGCTCAGGCAATgg                                                       <  1:1625362/70‑1 (MQ=255)
                 ttAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCgat                                                 >  1:4319657/1‑71 (MQ=255)
                 ttAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCgat                                                 >  1:26631/1‑71 (MQ=255)
                       gTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGAtttt                                           <  1:4301344/71‑1 (MQ=255)
                        tatataTCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGtt                                                                 <  1:2850330/48‑1 (MQ=255)
                        tatataTCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGtt                                                                 <  1:963255/48‑1 (MQ=255)
                        tatataTCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGc                                                            <  1:3361942/53‑1 (MQ=255)
                          tatatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCaa                                                          >  1:1882327/1‑53 (MQ=255)
                          tatatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGCTCAGGCaa                                                          >  1:2903749/1‑53 (MQ=255)
                            tatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTg                                       <  1:312639/70‑1 (MQ=255)
                            tatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTg                                       <  1:1942136/70‑1 (MQ=255)
                            tatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGa                                      >  1:1845766/1‑71 (MQ=255)
                            tatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGa                                      >  1:2129701/1‑71 (MQ=255)
                              tcatcTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTc                                                                >  1:4074848/1‑43 (MQ=255)
                              tcatcTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCgatgat                                              >  1:2880750/1‑61 (MQ=255)
                                atcTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGAttt                                   <  1:2404385/70‑1 (MQ=255)
                                atcTCTATCATCACAATGATAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTg                                  <  1:4085395/71‑1 (MQ=255)
                                 tctcTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCg                                                   <  1:3057836/53‑1 (MQ=255)
                                   tctATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGa                                      <  1:1448568/64‑1 (MQ=255)
                                   tctATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGAt                                     <  1:995413/65‑1 (MQ=255)
                                   tctATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTa                               >  1:3840859/1‑71 (MQ=255)
                                     tATCATCACAATGATAGCCGAAGATTTTGCCTGTTc                                                                <  1:1842592/36‑1 (MQ=255)
                                     tATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAtt                             >  1:2217980/1‑71 (MQ=255)
                                     tATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAtt                             >  1:1210945/1‑71 (MQ=255)
                                      atcatcACAATGATAGACGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGa                                      >  1:2625874/1‑61 (MQ=255)
                                       tcatcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGc                                                            <  1:2049267/38‑1 (MQ=255)
                                       tcatcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAtttt                           <  1:2380903/71‑1 (MQ=255)
                                       tcatcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAtttt                           <  1:376075/71‑1 (MQ=255)
                                       tcatcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAttt                            <  1:4304651/70‑1 (MQ=255)
                                       tcatcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAt                              <  1:3523883/68‑1 (MQ=255)
                                        catcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAttttt                          >  1:3497886/1‑71 (MQ=255)
                                         atcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGtt                                                     >  1:1728318/1‑43 (MQ=255)
                                         atcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTc                         >  1:783351/1‑71 (MQ=255)
                                         atcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTc                         >  1:4340371/1‑71 (MQ=255)
                                         atcaCAATGATAGCCGAAGATTTTGCCTGCTCAGGCAATTGTTCGATGATTTTTTTGATTTGTTATTTTTc                         <  1:3543396/71‑1 (MQ=255)
                                         atcaCAATGATAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTc                         >  1:2694936/1‑71 (MQ=255)
                                         atcaCAATGATAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTc                         <  1:2988882/71‑1 (MQ=255)
                                          tcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATgg                                                       <  1:3573354/40‑1 (MQ=255)
                                          tcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGt                                 <  1:3900633/62‑1 (MQ=255)
                                          tcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGt                                 <  1:4438745/62‑1 (MQ=255)
                                           cacaATGATAGCCGAAGATTTTGCCTGTTCAGGCAATgg                                                       <  1:4173859/39‑1 (MQ=255)
                                            acaATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCa                       <  1:2233636/70‑1 (MQ=255)
                                             caATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAttt                            <  1:522859/64‑1 (MQ=255)
                                              aaTGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACtt                    <  1:353620/71‑1 (MQ=255)
                                               aTGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACttt                   >  1:4278694/1‑71 (MQ=255)
                                               aTGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTT‑CACTTTc                  <  1:4369292/71‑1 (MQ=255)
                                                tGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACttt                   >  1:3013202/1‑70 (MQ=255)
                                                tGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTc                  <  1:2906631/71‑1 (MQ=255)
                                                tGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTc                  <  1:3887595/71‑1 (MQ=255)
                                                  aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGAt                                     <  1:2725145/50‑1 (MQ=255)
                                                  aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCa                 <  1:3256140/70‑1 (MQ=255)
                                                  aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                <  1:4502805/71‑1 (MQ=255)
                                                  aTAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCa                 <  1:2280202/70‑1 (MQ=255)
                                                   tAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCgatgat                                              >  1:1835110/1‑40 (MQ=255)
                                                    aGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTa              >  1:3695064/1‑71 (MQ=255)
                                                      ccGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGAtttt                                           <  1:1449156/40‑1 (MQ=255)
                                                       cGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTa              >  1:1531829/1‑68 (MQ=255)
                                                        gAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt          <  1:4333111/71‑1 (MQ=255)
                                                        gAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt          <  1:163593/71‑1 (MQ=255)
                                                         aaGATTTTGCCTGTTCAGGCAATGGTTCTATGATTTTTTTg                                       <  1:2341314/41‑1 (MQ=255)
                                                         aaGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTc                         <  1:1989430/55‑1 (MQ=255)
                                                           gATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACt                     <  1:1991837/57‑1 (MQ=255)
                                                           gATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAAt       >  1:4591750/1‑71 (MQ=255)
                                                           gATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAAt       >  1:3977956/1‑71 (MQ=255)
                                                           gATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAAt       >  1:2815151/1‑71 (MQ=255)
                                                            aTTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATg      <  1:2502560/71‑1 (MQ=255)
                                                             ttttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGc     <  1:691209/71‑1 (MQ=255)
                                                              tttGCCTGTTCAGGCAATGGTTCGATGAttttttt                                        >  1:1054601/1‑35 (MQ=255)
                                                              tttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTa                               >  1:1086352/1‑44 (MQ=255)
                                                              tttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTa                               >  1:2264950/1‑44 (MQ=255)
                                                              tttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTa                               >  1:358994/1‑44 (MQ=255)
                                                               ttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCAc                      >  1:1501347/1‑52 (MQ=255)
                                                               ttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCAc                      >  1:731728/1‑52 (MQ=255)
                                                                tGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTa         >  1:2381479/1‑64 (MQ=255)
                                                                 gCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCTTg  <  1:1238462/70‑1 (MQ=255)
                                                                   cTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCa                 <  1:2365014/53‑1 (MQ=255)
                                                                     gTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAAt       <  1:4177070/61‑1 (MQ=255)
                                                                      ttCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAttttt                          >  1:4379221/1‑41 (MQ=255)
                                                                      ttCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAttttt                          >  1:863393/1‑41 (MQ=255)
                                                                      ttCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt          >  1:4316382/1‑57 (MQ=255)
                                                                      ttCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTa         >  1:480356/1‑58 (MQ=255)
                                                                      |                                                                
CTTATGTTTTTGGTACATTAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCTTG  >  W3110S.gb/3633708‑3633842

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