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 3,712,033 G→A 31.8% M328I (ATG→ATA)  gidA → glucose‑inhibited cell‑division protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,712,0330GA31.8% 87.1 / 56.4 66M328I (ATG→ATA) gidAglucose‑inhibited cell‑division protein
Reads supporting (aligned to +/- strand):  ref base G (24/21);  new base A (10/11);  total (34/32)
Fisher's exact test for biased strand distribution p-value = 7.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.30e-01

ATGAAATTTATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCGATCCT  >  W3110S.gb/3711963‑3712099
                                                                      |                                                                  
aTGAAATTTATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATg                                                                    <  1:1179788/71‑1 (MQ=255)
 tGAAATTTATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGc                                                                   <  1:652162/71‑1 (MQ=255)
 tGAAATTTATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGc                                                                   <  1:2943179/71‑1 (MQ=255)
     aTTTATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAggg                                                               <  1:3402535/71‑1 (MQ=255)
     aTTTATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAggg                                                               <  1:554490/71‑1 (MQ=255)
       ttATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGa                                                             >  1:3071194/1‑71 (MQ=255)
        tATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGa                                                             >  1:3216946/1‑70 (MQ=255)
        tATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGCCCGCTCTATGCAgggg                                                              >  1:266452/1‑69 (MQ=255)
            cGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGaa                                                        <  1:1580786/71‑1 (MQ=255)
            cGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGaa                                                        <  1:2534068/71‑1 (MQ=255)
            cGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGa                                                         >  1:1307359/1‑70 (MQ=255)
                      ctcCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGaa                                                        <  1:788332/61‑1 (MQ=255)
                       tcCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAAcgcg                                                  >  1:1176784/1‑66 (MQ=255)
                       tcCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAAcgcg                                                  >  1:552094/1‑66 (MQ=255)
                       tcCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAAcgcg                                                  >  1:2082313/1‑66 (MQ=255)
                         caccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATc                                            >  1:1283303/1‑70 (MQ=255)
                         caccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATg                                                           <  1:292103/55‑1 (MQ=255)
                         caccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGAt                                             <  1:920351/69‑1 (MQ=255)
                         caccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGCAAAACGCGAAGAt                                             <  1:205687/69‑1 (MQ=255)
                           ccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGa                                                         >  1:2168210/1‑55 (MQ=255)
                           ccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGa                                                         >  1:2775590/1‑55 (MQ=255)
                           ccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGaa                                                >  1:3257774/1‑64 (MQ=255)
                           ccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGaa                                                >  1:4008544/1‑64 (MQ=255)
                           ccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGaa                                                >  1:1309647/1‑64 (MQ=255)
                             aGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCg                                       <  1:655741/71‑1 (MQ=255)
                             aGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCg                                       >  1:2621311/1‑71 (MQ=255)
                             aGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCg                                       >  1:1328203/1‑71 (MQ=255)
                             aGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGAt                                             >  1:1391504/1‑65 (MQ=255)
                                  gCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGaaaa                                                      >  1:1133817/1‑51 (MQ=255)
                                    cGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGt                                <  1:3294435/71‑1 (MQ=255)
                                    cGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGt                                <  1:1484582/71‑1 (MQ=255)
                                        cGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATg                            >  1:2667173/1‑71 (MQ=255)
                                        cGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATg                            >  1:599756/1‑71 (MQ=255)
                                         gATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGc                           <  1:3298638/71‑1 (MQ=255)
                                               cAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGaa                                                >  1:1511165/1‑44 (MQ=255)
                                               cAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGaa                                                >  1:2654798/1‑44 (MQ=255)
                                               cAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGaa                                                >  1:3569091/1‑44 (MQ=255)
                                               cAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGaa                                                >  1:345065/1‑44 (MQ=255)
                                               cAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGa                     <  1:2621182/71‑1 (MQ=255)
                                               cAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGa                     <  1:2328781/71‑1 (MQ=255)
                                                aGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGc                           <  1:737913/64‑1 (MQ=255)
                                                aGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAg                    <  1:1592669/71‑1 (MQ=255)
                                                aGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAg                    <  1:1490731/71‑1 (MQ=255)
                                                aGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAg                    <  1:167653/71‑1 (MQ=255)
                                                aGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAg                    <  1:1884146/71‑1 (MQ=255)
                                                  aTGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAg                    <  1:2866032/69‑1 (MQ=255)
                                                   tGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTAt                 <  1:983760/71‑1 (MQ=255)
                                                   tGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTAt                 <  1:1531039/71‑1 (MQ=255)
                                                   tGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTAt                 >  1:2160065/1‑71 (MQ=255)
                                                    gCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTa                  >  1:1284183/1‑69 (MQ=255)
                                                    gCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTAt                 >  1:1771740/1‑70 (MQ=255)
                                                    gCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTAt                 >  1:3238395/1‑70 (MQ=255)
                                                     cAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATg                <  1:2000508/70‑1 (MQ=255)
                                                       aaTCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCggg                                 <  1:1314914/51‑1 (MQ=255)
                                                       aaTCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCggg                                 <  1:1479349/51‑1 (MQ=255)
                                                        aTCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATc                                            >  1:1304548/1‑39 (MQ=255)
                                                        aTCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCg                                           >  1:1801663/1‑40 (MQ=255)
                                                        aTCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCg                                           >  1:3625590/1‑40 (MQ=255)
                                                        aTCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCg                                           >  1:42510/1‑40 (MQ=255)
                                                          cGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGActtct          >  1:2795324/1‑71 (MQ=255)
                                                              cGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCg       <  1:3539637/70‑1 (MQ=255)
                                                              cGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCg       <  1:1207525/70‑1 (MQ=255)
                                                              cGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCg       <  1:3108005/70‑1 (MQ=255)
                                                                ctctATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAg                    <  1:3307874/55‑1 (MQ=255)
                                                                  ctATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCGATTGAGTATGACTTCTTCGATCCt  >  1:2074310/1‑71 (MQ=255)
                                                                  ctATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCGATCCt  >  1:2345602/1‑71 (MQ=255)
                                                                     tGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGt                                <  1:1804538/38‑1 (MQ=255)
                                                                      |                                                                  
ATGAAATTTATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCGATCCT  >  W3110S.gb/3711963‑3712099

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