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 3,001,511 T→C 40.0% 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.gb3,001,5110TC40.0% 54.4 / 111.0 90I81T (ATA→ACA) xdhBxanthine dehydrogenase, FAD‑binding subunit
Reads supporting (aligned to +/- strand):  ref base T (36/18);  new base C (24/12);  total (60/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

CGGGGAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCG  >  W3110S.gb/3001444‑3001578
                                                                   |                                                                   
cGGGGAATTACGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCAAGCTAATaga                                                                  <  1:1824291/71‑1 (MQ=255)
         aCGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCta                                                          <  1:1129934/70‑1 (MQ=255)
         aCGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCta                                                          >  1:1240782/1‑70 (MQ=255)
         aCGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCta                                                          >  1:3117609/1‑70 (MQ=255)
         aCGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCta                                                          >  1:4473515/1‑70 (MQ=255)
         aCGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCta                                                          >  1:970347/1‑70 (MQ=255)
          cGCTGGCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCtat                                                         >  1:3013124/1‑70 (MQ=255)
               gCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATa                                                                    >  1:2530954/1‑54 (MQ=255)
               gCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGAt                                                              >  1:4344790/1‑60 (MQ=255)
               gCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGAt                                                              >  1:1521333/1‑60 (MQ=255)
               gCGGAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGAt                                                              >  1:4641082/1‑60 (MQ=255)
                 ggAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATaga                                                                  <  1:1704616/54‑1 (MQ=255)
                 ggAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATaga                                                                  <  1:4395595/54‑1 (MQ=255)
                 ggAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAAc                                                 <  1:3667171/71‑1 (MQ=255)
                  gAAGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATaga                                                                  <  1:25601/53‑1 (MQ=255)
                    aGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGt                                               >  1:522545/1‑70 (MQ=255)
                    aGATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGt                                               >  1:1407824/1‑70 (MQ=255)
                     gATGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATaga                                                                  <  1:2278502/50‑1 (MQ=255)
                       tGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATagaa                                                                 >  1:3405488/1‑49 (MQ=255)
                       tGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGAt                                                              <  1:4188457/52‑1 (MQ=255)
                       tGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGAt                                                              <  1:2371831/52‑1 (MQ=255)
                       tGGCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCtat                                                         >  1:1165722/1‑57 (MQ=255)
                        ggCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACagaa                                                                 >  1:820607/1‑48 (MQ=255)
                        ggCTCGCTACGTATCGGCTCTGCAACGACATTTACCAAGCTAATAGAAGATCCTATaa                                                       >  1:5090174/1‑58 (MQ=255)
                         gCTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCAtctc                                         >  1:2945412/1‑71 (MQ=255)
                          cTCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCAtct                                          >  1:839200/1‑69 (MQ=255)
                           tCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATagaa                                                                 >  1:2023949/1‑45 (MQ=255)
                           tCGCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATaa                                                       >  1:2526204/1‑55 (MQ=255)
                             gCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCAt                                            >  1:2015325/1‑64 (MQ=255)
                             gCTACGTATCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCAt                                            >  1:2009445/1‑64 (MQ=255)
                              cTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGc                                    <  1:3286547/71‑1 (MQ=255)
                              cTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGc                                    <  1:467790/71‑1 (MQ=255)
                              cTACGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGc                                    <  1:3414261/71‑1 (MQ=255)
                                 cGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGc                                    <  1:2372206/68‑1 (MQ=255)
                                 cGTATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGtt                                 <  1:204208/71‑1 (MQ=255)
                                   tATCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCa                                                   <  1:4043078/51‑1 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAATagaag                                                                >  1:2444203/1‑36 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAATagaag                                                                >  1:4399874/1‑36 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAATagaag                                                                >  1:1532067/1‑36 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAATagaa                                                                 >  1:5124002/1‑35 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAtgt                             >  1:3710183/1‑71 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAtgt                             >  1:3716015/1‑71 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAtgt                             >  1:3226150/1‑71 (MQ=255)
                                     tCGGCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCta                                                          >  1:2108180/1‑42 (MQ=255)
                                       ggCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCa                                             >  1:4014914/1‑53 (MQ=255)
                                       ggCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCAt                                            >  1:5007058/1‑54 (MQ=255)
                                       ggCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCg                                   >  1:2871118/1‑63 (MQ=255)
                                       ggCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgc                           >  1:3501352/1‑71 (MQ=255)
                                       ggCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAtgtg                            <  1:1630905/70‑1 (MQ=255)
                                        gCTCTGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgct                          <  1:3669830/71‑1 (MQ=255)
                                        gCTCTGCAACGACATTTACCCAGCTAACAGAAGATCCtat                                                         <  1:1982293/40‑1 (MQ=255)
                                          tctGCATCGACATTTACCCAGCTAACAGAAGATCCTATAACTc                                                    <  1:3329187/43‑1 (MQ=255)
                                            tGCAACGACATTTACCCAGCTAATAGAAGATCCtat                                                         <  1:3590412/36‑1 (MQ=255)
                                            tGCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGtgc                           <  1:2363327/66‑1 (MQ=255)
                                            tGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCgg                      >  1:3334805/1‑71 (MQ=255)
                                            tGCAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCgg                      >  1:619358/1‑71 (MQ=255)
                                             gCAACGACATTTCCCCAGCTAACAGAAGATCCTATAACTCAACGTCAt                                            >  1:3698478/1‑48 (MQ=255)
                                             gCAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     >  1:1909667/1‑71 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTGAt                                            >  1:4556794/1‑47 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCAt                                            >  1:3495332/1‑47 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCAt                                            >  1:5131149/1‑47 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCAt                                            >  1:495924/1‑47 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCAt                                            >  1:1515820/1‑47 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     <  1:349867/70‑1 (MQ=255)
                                              cAACGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTAAt                                            >  1:4551004/1‑47 (MQ=255)
                                              cAACGACATTTACCCAGCTAACAGAAGATCCTATaa                                                       >  1:3566324/1‑36 (MQ=255)
                                              cAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAtg                              <  1:3286731/61‑1 (MQ=255)
                                              cAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     >  1:546688/1‑70 (MQ=255)
                                              cAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     >  1:71356/1‑70 (MQ=255)
                                              cAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     >  1:3574396/1‑70 (MQ=255)
                                              cAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     >  1:2264860/1‑70 (MQ=255)
                                              cAACGACATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGc                     >  1:279849/1‑70 (MQ=255)
                                                aCGACATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCAc                  >  1:1789791/1‑71 (MQ=255)
                                                   aCATTTACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTc               <  1:4083792/71‑1 (MQ=255)
                                                   aCATTTACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTc               <  1:4155071/71‑1 (MQ=255)
                                                       ttACCCAGCTAACAGAAGATCCTATAACTCAACGTCAt                                            >  1:279106/1‑38 (MQ=255)
                                                       ttACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCAtt           >  1:2805557/1‑71 (MQ=255)
                                                        tACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCAtt           >  1:349715/1‑70 (MQ=255)
                                                        tACCCAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTg          >  1:427798/1‑71 (MQ=255)
                                                        tACCCAGCTAACTGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAt                               >  1:3421619/1‑50 (MQ=255)
                                                        tACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAt                               >  1:689452/1‑50 (MQ=255)
                                                        tACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTAt                               >  1:3518245/1‑50 (MQ=255)
                                                        tACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTg          >  1:728224/1‑71 (MQ=255)
                                                        tACCCAGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTg          >  1:1765850/1‑71 (MQ=255)
                                                           ccAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTg       <  1:983236/71‑1 (MQ=255)
                                                           ccAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTg       <  1:5016413/71‑1 (MQ=255)
                                                           ccAGCTAATAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTg       <  1:1142212/71‑1 (MQ=255)
                                                             aGCTAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGa     <  1:2651459/71‑1 (MQ=255)
                                                                tAACAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCg  >  1:1489764/1‑71 (MQ=255)
                                                                  aTAGAAGATCCTATAACTCAACGTCATCTTCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTg       <  1:4748208/64‑1 (MQ=255)
                                                                   tAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTa                                <  1:4001654/38‑1 (MQ=255)
                                                                   tAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCg  >  1:289322/1‑68 (MQ=255)
                                                                   tAGAAGATCCTATAACTCAACGTCATCTCCCGGCGTTATGTGCTGCGGCCACGTCCATTGCTGGACCg  >  1:18321/1‑68 (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