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 F17 I0 R1 87 56.5 4283937 98.6% 4223961 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,001,511 T→C 5.5% I81T (ATA→ACA)  xdhB → xanthine dehydrogenase, FAD‑binding subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,001,5110TC 5.5% 204.9 / 3.7 73I81T (ATA→ACA) xdhBxanthine dehydrogenase, FAD‑binding subunit
Reads supporting (aligned to +/- strand):  ref base T (37/32);  new base C (2/2);  total (39/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

CGGGGAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCG  >  W3110S.gb/3001444‑3001578
                                                                   |                                                                   
cGGGGAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATaga                                                                  <  1:2503097/71‑1 (MQ=255)
cGGGGAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATaga                                                                  <  1:3302695/71‑1 (MQ=255)
cGGGGAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATaga                                                                  <  1:2301693/71‑1 (MQ=255)
cGGGGAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATag                                                                   >  1:854994/1‑70 (MQ=255)
     aaTTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATc                                                             >  1:1674974/1‑71 (MQ=255)
      aTTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATc                                                             <  1:1593663/70‑1 (MQ=255)
         aCGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCta                                                          >  1:2675833/1‑70 (MQ=255)
         aCGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCta                                                          >  1:31602/1‑70 (MQ=255)
         aCGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCta                                                          >  1:1861427/1‑70 (MQ=255)
          cGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCtat                                                         <  1:814379/70‑1 (MQ=255)
             tGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAAc                                                      >  1:2741611/1‑70 (MQ=255)
               gCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTc                                                    >  1:2492754/1‑70 (MQ=255)
               gCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTc                                                    >  1:3190553/1‑70 (MQ=255)
                cGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACagaaga                                                               <  1:161425/58‑1 (MQ=255)
                 ggAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAAc                                                 >  1:4208531/1‑71 (MQ=255)
                    aGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTc                                              <  1:3647392/71‑1 (MQ=255)
                     gATGGCTCGCTACGTATCGGCTCTGTAACGACATTTACCCAGCTAATAGAAGATc                                                             <  1:3277597/55‑1 (MQ=255)
                     gATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCtat                                                         <  1:1440684/59‑1 (MQ=255)
                          cTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATagaa                                                                 >  1:3242237/1‑46 (MQ=255)
                            cGCTACGTATCGTCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCg                                      >  1:1068567/1‑71 (MQ=255)
                            cGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCg                                      >  1:632923/1‑71 (MQ=255)
                            cGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCg                                      >  1:2081397/1‑71 (MQ=255)
                             gCTACGAATCGGCTCTGCAACGACATTTACCCAGCTAATagaa                                                                 >  1:549996/1‑43 (MQ=255)
                               tACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCgg                                     <  1:3280217/69‑1 (MQ=255)
                                aCGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCa                                                   >  1:3724681/1‑54 (MQ=255)
                                aCGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGt                                  >  1:3617718/1‑71 (MQ=255)
                                 cGTATCGGCTCTGCAACGACATTTACCCAGCTAATagaag                                                                >  1:4000248/1‑40 (MQ=255)
                                 cGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCaa                                                  >  1:3249792/1‑54 (MQ=255)
                                 cGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCg                                   <  1:1645635/69‑1 (MQ=255)
                                 cGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGt                                  <  1:2465326/70‑1 (MQ=255)
                                  gTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGt                                  <  1:383846/69‑1 (MQ=255)
                                  gTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTa                                <  1:1879052/71‑1 (MQ=255)
                                  gTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTa                                >  1:1374361/1‑71 (MQ=255)
                                   tATCGGCTCTGCAACGACATTTACCCAGCTAATagaa                                                                 >  1:4273824/1‑37 (MQ=255)
                                   tATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATc                                                             <  1:613870/41‑1 (MQ=255)
                                   tATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGc                                    <  1:1594828/66‑1 (MQ=255)
                                   tATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAt                               >  1:4162341/1‑71 (MQ=255)
                                   tATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAt                               >  1:2158667/1‑71 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCt                                                           <  1:570799/41‑1 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTcc                                        <  1:2657526/60‑1 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTcc                                        <  1:1821482/60‑1 (MQ=255)
                                        gCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGtt                                 <  1:1703445/64‑1 (MQ=255)
                                        gCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgct                          <  1:364475/71‑1 (MQ=255)
                                            tGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTc                                                    <  1:3507932/41‑1 (MQ=255)
                                            tGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAtg                              <  1:2444765/63‑1 (MQ=255)
                                            tGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgctgc                        <  1:654388/69‑1 (MQ=255)
                                            tGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCgg                      >  1:2797989/1‑71 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCgg                      <  1:2974203/69‑1 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     >  1:138538/1‑70 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     >  1:2562344/1‑70 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     >  1:406193/1‑70 (MQ=255)
                                              cAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     >  1:1558267/1‑70 (MQ=255)
                                               aaCGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCAtct                                          <  1:3727756/48‑1 (MQ=255)
                                                aCGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCAc                  <  1:1927038/71‑1 (MQ=255)
                                                 cGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACg                 >  1:2393378/1‑71 (MQ=255)
                                                 cGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACg                 >  1:255753/1‑71 (MQ=255)
                                                   aCATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTc               >  1:865166/1‑71 (MQ=255)
                                                   aCATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTc               >  1:2870504/1‑71 (MQ=255)
                                                   aCATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTc               >  1:2539163/1‑71 (MQ=255)
                                                    cATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAtgtg                            >  1:903835/1‑57 (MQ=255)
                                                     aTTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAtgt                             <  1:3868940/55‑1 (MQ=255)
                                                       ttACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAtg                              <  1:931782/52‑1 (MQ=255)
                                                         aCCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCAc                  >  1:3638100/1‑62 (MQ=255)
                                                          cccAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCt        <  1:2462583/71‑1 (MQ=255)
                                                           ccAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCt        >  1:3468017/1‑70 (MQ=255)
                                                            cAGCTAATAGAAGATCCTATTACTCAACGTCATCTCCCgg                                     <  1:946898/40‑1 (MQ=255)
                                                             aGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGa     >  1:1566451/1‑71 (MQ=255)
                                                              gCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAtg                              <  1:2331900/45‑1 (MQ=255)
                                                               cTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGt                                  <  1:979024/40‑1 (MQ=255)
                                                                tAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCg  >  1:1813819/1‑71 (MQ=255)
                                                                tAATAGAAGATCATATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCg  >  1:3431141/1‑71 (MQ=255)
                                                                  aTAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCg  <  1:3074462/69‑1 (MQ=255)
                                                                  aTAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCg  >  1:247937/1‑69 (MQ=255)
                                                                   tAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgct                          <  1:609270/44‑1 (MQ=255)
                                                                   tAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGt                <  1:3283554/54‑1 (MQ=255)
                                                                   |                                                                   
CGGGGAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCG  >  W3110S.gb/3001444‑3001578

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