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 4,014,473 T→C 35.6% L287P (CTG→CCG)  yhhJ → predicted transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,014,4730TC35.6% 53.5 / 61.1 59L287P (CTG→CCG) yhhJpredicted transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (14/24);  new base C (11/10);  total (25/34)
Fisher's exact test for biased strand distribution p-value = 2.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

GCGCTCAGTCTGTTTGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTCCACGCCGCGCGAAAG  >  W3110S.gb/4014403‑4014542
                                                                      |                                                                     
gcgcTCAGTCTGTTTGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACt                                                                       >  1:4313393/1‑71 (MQ=255)
  gcTCAGTCTGTTTGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCgg                                                                     <  1:3911239/71‑1 (MQ=255)
       gTCTGTTTGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTggg                                                                    <  1:1434980/67‑1 (MQ=255)
       gTCTGTTTGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTggg                                                                    <  1:644904/67‑1 (MQ=255)
       gTCTGTTTGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTggg                                                                    <  1:3046473/67‑1 (MQ=255)
       gTCTGTTTGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTggg                                                                    <  1:2615233/67‑1 (MQ=255)
       gTCTGTTTGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGgctg                                                                <  1:2730644/71‑1 (MQ=255)
        tCTGTTTGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCgg                                                                     <  1:4688639/65‑1 (MQ=255)
            tttGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGACGCAACCGGGGCTGCTGGt                                                           >  1:738089/1‑71 (MQ=255)
            tttGCCACCAAGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGGCTGCTGGt                                                           >  1:4913426/1‑71 (MQ=255)
               gCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGGCTGCTGGTGa                                                         <  1:4101701/70‑1 (MQ=255)
                 caccacGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGGCTGCTGGTGATTc                                                      <  1:660510/71‑1 (MQ=255)
                  accacGTCAATCGTCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCt                                                     <  1:4182504/71‑1 (MQ=255)
                  accacGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCt                                                     >  1:2402943/1‑71 (MQ=255)
                   ccacGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGgc                                                                  <  1:2948500/57‑1 (MQ=255)
                    cacGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTgg                                                   <  1:1570728/71‑1 (MQ=255)
                     acGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTTATTCTGGt                                                  <  1:1065021/71‑1 (MQ=255)
                     acGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGt                                                  <  1:4420847/71‑1 (MQ=255)
                     acGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGGCTGCTGGTGATTCTGGt                                                  >  1:4074408/1‑71 (MQ=255)
                     acGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGGCTGCTGGTGATTCTGGt                                                  >  1:1760929/1‑71 (MQ=255)
                        tCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGtgct                                               <  1:1246586/71‑1 (MQ=255)
                         cAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGt                                                  >  1:883883/1‑67 (MQ=255)
                          aaTCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGtgctgc                                             >  1:4506534/1‑71 (MQ=255)
                           aTCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGtgctgct                                            <  1:744228/71‑1 (MQ=255)
                             cGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGtgctgctgc                                          >  1:674519/1‑71 (MQ=255)
                             cGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGtgctgctgc                                          >  1:2359385/1‑71 (MQ=255)
                             cGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGtgctgctg                                           <  1:4970648/70‑1 (MQ=255)
                              ggCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTgg                                                   >  1:4386631/1‑61 (MQ=255)
                               gCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGgctgct                                                              <  1:3995199/49‑1 (MQ=255)
                                 aTTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGGCTGCTgg                                                            >  1:4594172/1‑49 (MQ=255)
                                  tttttATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGGCTGCTGGTGAt                                                        <  1:4844416/52‑1 (MQ=255)
                                    tttATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTgg                                                   >  1:610627/1‑55 (MQ=255)
                                    tttATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTgg                                                   >  1:388465/1‑55 (MQ=255)
                                    tttATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGc                                    >  1:1127730/1‑70 (MQ=255)
                                    tttATGGGGACGATAGCGCGTTCAATGCCGCAACCGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGc                                    >  1:3479326/1‑70 (MQ=255)
                                    tttATGGGGAAGATAGCGCGTTCAATGCCGCAACCGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGc                                    >  1:4804099/1‑70 (MQ=255)
                                     ttATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCa                                   <  1:2696636/70‑1 (MQ=255)
                                              cGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGaaaa                                 >  1:2287870/1‑63 (MQ=255)
                                              cGATAGCGCGTTCAATGCCGCAACCGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTcc                         <  1:5044003/71‑1 (MQ=255)
                                                aTAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCa                                   <  1:241855/59‑1 (MQ=255)
                                                aTAGCGCGTTCAATGCCGCAACCGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCgg                       >  1:2683076/1‑71 (MQ=255)
                                                 tAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCggt                      <  1:4142518/71‑1 (MQ=255)
                                                  aGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCggt                      <  1:2364747/70‑1 (MQ=255)
                                                  aGCGCGTTCAATGCCGCAACCGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCg                        >  1:3431879/1‑68 (MQ=255)
                                                    cgcgTTCAATGCCGCAACCGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCggtgg                    <  1:44857/70‑1 (MQ=255)
                                                     gcgTTAAATGCCGCAACTGGGGCTGCTGGTGATTCTg                                                    >  1:2112826/1‑37 (MQ=255)
                                                      cgTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTc                 <  1:4520510/71‑1 (MQ=255)
                                                       gTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTcc                         <  1:1461949/62‑1 (MQ=255)
                                                        ttCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTCCa               <  1:4719883/71‑1 (MQ=255)
                                                         tCAATGCCGCAACTGGGGCTGCTTGTGATTCTGGTGCTGCTGCCGCTGCAAATGCtt                            <  1:909855/57‑1 (MQ=255)
                                                            aTGCCGCAACTGGGGCTTCTGGTGATTCTGGtgctgc                                             >  1:1516316/1‑37 (MQ=255)
                                                            aTGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTCCAcgcc           >  1:2196210/1‑71 (MQ=255)
                                                             tGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCa                                   <  1:1269387/46‑1 (MQ=255)
                                                             tGCCGCAACCGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTCCa               >  1:2089289/1‑66 (MQ=255)
                                                               ccGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCaaa                                 >  1:267996/1‑46 (MQ=255)
                                                               ccGCAACCGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTCCACGCcgcg        >  1:3982046/1‑71 (MQ=255)
                                                                cGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAAt                                <  1:3072507/46‑1 (MQ=255)
                                                                     cTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTCCACGCCGCGCGAAAg  <  1:4913014/71‑1 (MQ=255)
                                                                     cTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTCCACGCCGCGCGAAAg  <  1:2978083/71‑1 (MQ=255)
                                                                     cTGCGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTCCACGCCGCGCGAAAg  <  1:62191/71‑1 (MQ=255)
                                                                      tGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTCCACGCCGCGCGAAAg  >  1:4180407/1‑70 (MQ=255)
                                                                      |                                                                     
GCGCTCAGTCTGTTTGCCACCACGTCAATCGGCATTTTTATGGGGACGATAGCGCGTTCAATGCCGCAACTGGGGCTGCTGGTGATTCTGGTGCTGCTGCCGCTGCAAATGCTTTCCGGTGGTTCCACGCCGCGCGAAAG  >  W3110S.gb/4014403‑4014542

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