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 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,343,341 T→C 23.1% I36T (ATC→ACC)  yhbN → predicted transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,343,3410TC23.1% 122.5 / 38.0 65I36T (ATC→ACC) yhbNpredicted transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (29/21);  new base C (10/5);  total (39/26)
Fisher's exact test for biased strand distribution p-value = 7.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

CAGCTCACTTCTGGCCGCCAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTACCGGTAATGTC  >  W3110S.gb/3343279‑3343408
                                                              |                                                                   
cAGCTCACTTCTGGCCGCCAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTg                                                             <  1:1310155/71‑1 (MQ=255)
cAGCTCACTTCTGGCC‑CCAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGa                                                            <  1:1415428/71‑1 (MQ=255)
  gCTCACTTCTGGCCGCCAGCATTCCGGCATTTGCCGTAACCGGAGACACTTATCAGCCGACCCACATTg                                                             <  1:4041705/69‑1 (MQ=255)
  gCTCACTTCTGGCCGCCAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGACCCACATTg                                                             <  1:2875032/69‑1 (MQ=255)
  gCTCACTTCTGGCCGCCAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGACCCACATTg                                                             <  1:1798108/69‑1 (MQ=255)
     cACTTCTGGCCGCCAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCg                                                        >  1:176838/1‑71 (MQ=255)
      aCTTCTGGCCGCCAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATc                                                         <  1:2684616/69‑1 (MQ=255)
          cTGGCCGCCAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGAc                                                     >  1:1620545/1‑69 (MQ=255)
             gccgccAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGACCCACATTGAATCGGACCAGCa                                                <  1:751402/71‑1 (MQ=255)
                gccAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAAtc                                             >  1:3968628/1‑71 (MQ=255)
                gccAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAAtc                                             >  1:3750150/1‑71 (MQ=255)
                      aTTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGACCCACATTGAATCGGACCAGCAATCTCTTGa                                       >  1:2733129/1‑71 (MQ=255)
                         ccGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCgg                                                       >  1:1014326/1‑52 (MQ=255)
                         ccGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGatat                                    >  1:1494244/1‑71 (MQ=255)
                         ccGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGatat                                    >  1:1865090/1‑71 (MQ=255)
                          cGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGatat                                    <  1:2205044/70‑1 (MQ=255)
                            gCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGAcc                                                    >  1:107023/1‑52 (MQ=255)
                               tttGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCa                                                <  1:1218132/53‑1 (MQ=255)
                               tttGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCa                                                <  1:2728435/53‑1 (MQ=255)
                               tttGCCGTAACCGGAGACACTGATCAGCCGACCCACATTGAATCGGACCAGc                                                 <  1:470765/52‑1 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAAt                                              >  1:3239679/1‑53 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAAt                                              >  1:207337/1‑53 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGata                                     >  1:3252512/1‑62 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGata                                     >  1:2947714/1‑62 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAg                               >  1:2765894/1‑68 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGc                             <  1:600876/70‑1 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGC‑ATCTCTTGATATGCAAGGCa                            <  1:2007395/70‑1 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGACCCACATTGAATCGGCCCAGCAATCTCTTGATATGCAAGGc                             >  1:1739662/1‑70 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGACCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGc                             >  1:3469335/1‑70 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGACCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGc                             >  1:893856/1‑70 (MQ=255)
                                 tGCCGTAACCGGAGACACTGATCAGCCGACCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGc                             >  1:3536347/1‑70 (MQ=255)
                                   ccGTAACCGGAGACACTGATCAGCCGATCCACATTGAATc                                                         >  1:3334241/1‑40 (MQ=255)
                                   ccGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAAc                          >  1:1048332/1‑71 (MQ=255)
                                      tAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGTAAccac                       <  1:2138188/71‑4 (MQ=255)
                                      tAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTg                       <  1:3891818/71‑1 (MQ=255)
                                        aCCGGAGACACTGATCAGCCGATCCACATTGAATCGTACCAGCAATCTCTTGATATg                                   >  1:245895/1‑57 (MQ=255)
                                        aCCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCaa                                               >  1:4004620/1‑45 (MQ=255)
                                        aCCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATg                                   >  1:2175012/1‑57 (MQ=255)
                                        aCCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGt                     >  1:3112137/1‑71 (MQ=255)
                                           ggAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTAc                  <  1:2962873/71‑1 (MQ=255)
                                               acacTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCtt                                         <  1:2099908/44‑1 (MQ=255)
                                                cacTGATCAGCCGACCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTa             >  1:3362159/1‑71 (MQ=255)
                                                cacTGATCAGCCGACCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTa             >  1:3384317/1‑71 (MQ=255)
                                                cacTGATCAGCCGACCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTa             >  1:3388900/1‑71 (MQ=255)
                                                cacTGATCAGCCGACCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTa             >  1:4052099/1‑71 (MQ=255)
                                                 acTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTAc                  >  1:2615952/1‑65 (MQ=255)
                                                 acTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTAc                  >  1:2607043/1‑65 (MQ=255)
                                                 acTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTAc                  >  1:1031787/1‑65 (MQ=255)
                                                 acTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTAc                  >  1:1231385/1‑65 (MQ=255)
                                                 acTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTAc            >  1:1498025/1‑71 (MQ=255)
                                                 acTGATCAGCCGACCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTAc            >  1:2056210/1‑71 (MQ=255)
                                                  cTGATCAGCCGATCCACATTGAATCGGACCAGCAAtc                                             <  1:210819/37‑1 (MQ=255)
                                                  cTGATCAGCCGATCCACATTGAATCGGACCAGCAAtc                                             <  1:3720426/37‑1 (MQ=255)
                                                  cTGATCAGCCGATCCACATTGAATCGGACCAGCAAtc                                             <  1:2488220/37‑1 (MQ=255)
                                                  cTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTAcc           >  1:412456/1‑71 (MQ=255)
                                                  cTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTAcc           >  1:1028040/1‑71 (MQ=255)
                                                   tGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTAcct          >  1:847952/1‑70 (MQ=255)
                                                    gATCAGCCGATCCACATTGAATCGGACCAGCAAtctc                                           >  1:3405822/1‑37 (MQ=255)
                                                     aTCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTACCGGt        <  1:3796675/71‑1 (MQ=255)
                                                     aTCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTACCGGt        <  1:1906312/71‑1 (MQ=255)
                                                      tCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTACCGGTa       <  1:2329325/71‑1 (MQ=255)
                                                       cAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTgg                      >  1:921636/1‑55 (MQ=255)
                                                           cGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTTGTTACCTTTACCGGTAATGTc  <  1:3597418/71‑1 (MQ=255)
                                                             aTCCACATTGAATCGGACCAGCAATCTCTTGATATGCTAGGCa                            <  1:3596639/43‑1 (MQ=255)
                                                             aTCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCa                            <  1:2753523/43‑1 (MQ=255)
                                                              |                                                                   
CAGCTCACTTCTGGCCGCCAGCATTCCGGCATTTGCCGTAACCGGAGACACTGATCAGCCGATCCACATTGAATCGGACCAGCAATCTCTTGATATGCAAGGCAACGTGGTTACCTTTACCGGTAATGTC  >  W3110S.gb/3343279‑3343408

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