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 3,516,285 T→C 33.4% intergenic (+20/‑47) hslU → / → menA molecular chaperone and ATPase component of HslUV protease/1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,516,2850TC33.4% 81.9 / 68.2 73intergenic (+20/‑47)hslU/menAmolecular chaperone and ATPase component of HslUV protease/1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase
Reads supporting (aligned to +/- strand):  ref base T (22/26);  new base C (12/12);  total (35/38)
Fisher's exact test for biased strand distribution p-value = 8.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGATGCGTTGGTGGCAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAATTAGCCG  >  W3110S.gb/3516219‑3516354
                                                                  |                                                                     
tGGATGCGTTGGTGGCAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCAtt                                                                   >  1:247684/1‑71 (MQ=255)
    tGCGTTGGTGGCAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGttt                                                               <  1:126028/71‑1 (MQ=255)
    tGCGTTGGTGGCAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGt                                                                 >  1:1718703/1‑69 (MQ=255)
      cGTTGGTGGCAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGa                                                             <  1:2336137/71‑1 (MQ=255)
       gTTGGTGGCAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGa                                                             >  1:3890022/1‑70 (MQ=255)
        ttGGTGGCAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGAt                                                            <  1:304900/70‑1 (MQ=255)
               cAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTg                                                     >  1:4109401/1‑70 (MQ=255)
               cAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGa                                                    <  1:872844/71‑1 (MQ=255)
               cAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGa                                                    <  1:1380852/71‑1 (MQ=255)
               cAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGa                                                    <  1:1109249/71‑1 (MQ=255)
               cAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTg                                                     <  1:2575397/70‑1 (MQ=255)
                aGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGaa                                                   <  1:2367378/71‑1 (MQ=255)
                 gATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTcaccat                                                                    <  1:5078143/53‑1 (MQ=255)
                  aTGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGaa                                                   <  1:1281655/69‑1 (MQ=255)
                    gAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGa                                                             >  1:1833530/1‑57 (MQ=255)
                    gAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGAAAGGc                                               >  1:1331875/1‑71 (MQ=255)
                    gAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCAATGTTTGATGGGGCTGAAAg                                                 >  1:3055430/1‑69 (MQ=255)
                     aaGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGAAAGGcc                                              >  1:865363/1‑71 (MQ=255)
                     aaGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGAAAGGcc                                              >  1:683882/1‑71 (MQ=255)
                        aTCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGa                                                    <  1:4658135/62‑1 (MQ=255)
                         tCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGTGGCTGAAAGGCCCCAt                                          >  1:4563414/1‑71 (MQ=255)
                         tCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCAt                                          >  1:4483400/1‑71 (MQ=255)
                         tCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGAAAGGCCCCAt                                          >  1:1433229/1‑71 (MQ=255)
                          cTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATggg                                                         >  1:1232261/1‑55 (MQ=255)
                          cTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCATTGttt                                                               >  1:2926804/1‑49 (MQ=255)
                          cTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGaa                                                   >  1:1588153/1‑61 (MQ=255)
                          cTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCAACATTGTTTGATGGGGCTGaaa                                                  >  1:1598516/1‑62 (MQ=255)
                             aGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCAtttt                                       <  1:5026989/70‑1 (MQ=255)
                             aGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCAtttt                                       <  1:4994018/70‑1 (MQ=255)
                             aGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCAtttt                                       >  1:1698703/1‑70 (MQ=255)
                             aGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCAtttt                                       <  1:2604707/70‑1 (MQ=255)
                             aGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCAtttt                                       <  1:2735893/70‑1 (MQ=255)
                             aGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCAtttt                                       <  1:314509/70‑1 (MQ=255)
                             aGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGAAAGGCCCCAtttt                                       <  1:4689024/70‑1 (MQ=255)
                                 gTTTTATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTg                                  <  1:3320913/71‑1 (MQ=255)
                                  ttttATCCTATAATCGCGTTCAATCATTTTCATCATTGtt                                                                <  1:1198145/40‑1 (MQ=255)
                                  ttttATCCTATAATCGCGTTCAATCATTTTCATCATTGtt                                                                <  1:832832/40‑1 (MQ=255)
                                  ttttATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTg                                                              <  1:3486232/42‑1 (MQ=255)
                                  ttttATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGa                                                    <  1:4455130/52‑1 (MQ=255)
                                    ttATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTg                                                              >  1:2844131/1‑40 (MQ=255)
                                    ttATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGa                                                    >  1:1283242/1‑50 (MQ=255)
                                    ttATCCTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGAAAGGCCCCAtt                                         >  1:1187239/1‑61 (MQ=255)
                                         cTATAATCGCGTTCAATCATTTTCACCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGtat                          <  1:3143659/71‑1 (MQ=255)
                                          tataATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCAtttt                                       <  1:4606689/57‑1 (MQ=255)
                                          tataATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCAtttt                                       <  1:339956/57‑1 (MQ=255)
                                          tataATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGta                           <  1:2295912/69‑1 (MQ=255)
                                           ataATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGtatta                        >  1:3114202/1‑71 (MQ=255)
                                            taATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTAt                                    <  1:1424712/58‑1 (MQ=255)
                                            taATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGtattat                       >  1:2823689/1‑71 (MQ=255)
                                            taATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGtattat                       >  1:2783705/1‑71 (MQ=255)
                                            taATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGtattat                       >  1:3222511/1‑71 (MQ=255)
                                            taATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGtatta                        >  1:872443/1‑70 (MQ=255)
                                              aTCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGa                                                    <  1:71186/40‑1 (MQ=255)
                                               tCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGa                                                    <  1:1842359/39‑1 (MQ=255)
                                                 gcgTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTg                  <  1:941834/71‑1 (MQ=255)
                                                     tCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGaac               >  1:2618323/1‑70 (MQ=255)
                                                     tCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGaac               >  1:368083/1‑70 (MQ=255)
                                                     tCAATCATTTTCACCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGaac               >  1:4676374/1‑70 (MQ=255)
                                                      cAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGta                           >  1:3265075/1‑57 (MQ=255)
                                                       aaTCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGtatt                         <  1:2274414/58‑1 (MQ=255)
                                                          cATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTa                                     >  1:4362612/1‑43 (MQ=255)
                                                           aTTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAAt        <  1:2985042/71‑1 (MQ=255)
                                                           aTTTTCACCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTgg                                 >  1:3061317/1‑46 (MQ=255)
                                                           aTTTTCACCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTgg                                 >  1:5022776/1‑46 (MQ=255)
                                                           aTTTTCACCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAAt        <  1:1656439/71‑1 (MQ=255)
                                                           aTTTTCACCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAAt        <  1:1650372/71‑1 (MQ=255)
                                                              ttCATCCTTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGcgcg                             >  1:658677/1‑47 (MQ=255)
                                                              ttCATCATTGTTTGATGGGGCTGAAAGGCCCCAttttt                                      <  1:1789150/38‑1 (MQ=255)
                                                              ttCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTa                                     <  1:4988403/39‑1 (MQ=255)
                                                              ttCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGcgcg                             >  1:1156516/1‑47 (MQ=255)
                                                              ttCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGcgcg                             >  1:1061735/1‑47 (MQ=255)
                                                              ttCACCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTTGCGCGTATTATGACTGAACAACAAATTa      <  1:4499039/70‑1 (MQ=255)
                                                              ttCACCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAATTa      <  1:1997396/70‑1 (MQ=255)
                                                              ttCACCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAATTa      <  1:1102120/70‑1 (MQ=255)
                                                               tcatcaTTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAATTAg     <  1:1598573/70‑1 (MQ=255)
                                                                catcatTGTTTTATGGGGCTGAAAGGCCCCAtttt                                       <  1:105889/35‑1 (MQ=255)
                                                                catcatTGTTTGATGGGGCTGAAAGGCCCCAtttt                                       <  1:5064267/35‑1 (MQ=255)
                                                                catcatTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAATTAGcc   >  1:1556242/1‑71 (MQ=255)
                                                                 atcatTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAATTAGCCg  <  1:1612762/71‑1 (MQ=255)
                                                                  tcatTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAATTAGCCg  >  1:1374598/1‑70 (MQ=255)
                                                                  |                                                                     
TGGATGCGTTGGTGGCAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGTTTGATGGGGCTGAAAGGCCCCATTTTTATTGGCGCGTATTATGACTGAACAACAAATTAGCCG  >  W3110S.gb/3516219‑3516354

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