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 3,727,747 T→C 34.5% V168V (GTT→GTC)  pstA → phosphate transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,727,7470TC34.5% 58.4 / 56.9 58V168V (GTT→GTC) pstAphosphate transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (21/17);  new base C (12/8);  total (33/25)
Fisher's exact test for biased strand distribution p-value = 7.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

GGCGCAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTGGGT  >  W3110S.gb/3727678‑3727816
                                                                     |                                                                     
ggCGCAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTa                                                                      >  1:4285790/1‑71 (MQ=255)
 gcgcAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTCAt                                                                     <  1:4220267/71‑1 (MQ=255)
 gcgcAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTCAt                                                                     <  1:4495509/71‑1 (MQ=255)
  cgcAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTCATc                                                                    <  1:267318/71‑1 (MQ=255)
        tGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATc                                                                    <  1:2511337/65‑1 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTa                                                                      >  1:4556232/1‑53 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTa                                                                      >  1:455411/1‑53 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTa                                                                      >  1:597630/1‑53 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTa                                                                      >  1:3571702/1‑53 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTa                                                                      >  1:1233005/1‑53 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACa                                                    >  1:1155520/1‑71 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACa                                                    >  1:2336613/1‑71 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTCATCCGCACCACCGAGAACa                                                    >  1:4743329/1‑71 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTCATCCGCACCACCGAGAACa                                                    >  1:4461091/1‑71 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGAAGGTGCCGATTGTCATCCGCACCACCGAGAACa                                                    >  1:4505565/1‑71 (MQ=255)
                        cTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGa                                              <  1:4057904/71‑1 (MQ=255)
                        cTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGa                                              <  1:992182/71‑1 (MQ=255)
                           ggcgggcgTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGaa                                             <  1:1508626/69‑1 (MQ=255)
                            gcgggcgTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACt                                          <  1:177656/71‑1 (MQ=255)
                            gcgggcgTGATTGCCCTGGCGGTGTTGCAGGTGCCGATTGTTa                                                                      <  1:2225418/43‑1 (MQ=255)
                            gcgggcgTGATTGCCCTGGCGGTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAAc                                           <  1:4673812/70‑1 (MQ=255)
                             cgggcgTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTg                                         <  1:2265289/71‑1 (MQ=255)
                                 cgTGATTGCCCTGGCGTTGTTGCAGGTGCAGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGc                                     <  1:2168761/71‑1 (MQ=255)
                                     aTTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTa                                 >  1:1337942/1‑71 (MQ=255)
                                     aTTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTa                                 >  1:3908089/1‑71 (MQ=255)
                                     aTTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTa                                 >  1:2771031/1‑71 (MQ=255)
                                       tGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTa                                 >  1:836853/1‑69 (MQ=255)
                                       tGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTa                                 >  1:4321894/1‑69 (MQ=255)
                                        gCCCTGGCGTTGTTGCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTg                                         >  1:3471773/1‑60 (MQ=255)
                                        gCCCTGGCGTTGTTGCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACa                               <  1:4611210/70‑1 (MQ=255)
                                        gCCCTGGCGTTGTTGCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAg                              >  1:845198/1‑71 (MQ=255)
                                           cTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGaa                                                      <  1:3987519/44‑1 (MQ=255)
                                           cTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCg                                   <  1:567462/63‑1 (MQ=255)
                                            tGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTg                          >  1:2123980/1‑71 (MQ=255)
                                            tGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTg                          >  1:4872491/1‑71 (MQ=255)
                                              gCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGa                                              <  1:4833583/49‑1 (MQ=255)
                                              gCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGa                                              <  1:377263/49‑1 (MQ=255)
                                                 ttgttgCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTg                                               <  1:1443469/45‑1 (MQ=255)
                                                 ttgttgCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTg                                               <  1:5057779/45‑1 (MQ=255)
                                                 ttgttgCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACa                               <  1:2893527/61‑1 (MQ=255)
                                                   gttgCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGa                                              <  1:1352815/44‑1 (MQ=255)
                                                   gttgCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGa                                              <  1:4261830/44‑1 (MQ=255)
                                                   gttgCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGt                       <  1:935836/67‑1 (MQ=255)
                                                   gttgCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTTCAGCCTGCGTGAAg                   >  1:653860/1‑71 (MQ=255)
                                                   gttgCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGc                             >  1:4508484/1‑61 (MQ=255)
                                                   gttgCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGc                             >  1:540191/1‑61 (MQ=255)
                                                   gttgCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAg                   >  1:1820857/1‑71 (MQ=255)
                                                      gCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCgg                >  1:2489469/1‑71 (MQ=255)
                                                      gCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCgg                >  1:2437426/1‑71 (MQ=255)
                                                      gCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCg                 >  1:1368562/1‑70 (MQ=255)
                                                       cAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGc               >  1:4665099/1‑71 (MQ=255)
                                                           tGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAg                              >  1:3559312/1‑52 (MQ=255)
                                                           tGCCGATTGTCATCCGCACCACCGAGAACATGCTGaa                                             <  1:3765533/37‑1 (MQ=255)
                                                              cGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATgcg        >  1:308987/1‑71 (MQ=255)
                                                                aTTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTa                                 >  1:3762176/1‑44 (MQ=255)
                                                                  tGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTgg    >  1:3297348/1‑71 (MQ=255)
                                                                  tGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTgg    >  1:3291640/1‑71 (MQ=255)
                                                                  tGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTg     <  1:1543783/70‑1 (MQ=255)
                                                                    ttATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTGGGt  <  1:3042580/71‑1 (MQ=255)
                                                                     |                                                                     
GGCGCAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTGGGT  >  W3110S.gb/3727678‑3727816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A