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 F28 I1 R2 328 63.0 4687567 98.0% 4593815 65.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 3,591,880 C→T M201I (ATG→ATA)  yihF ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,591,8800CT100.0% 253.8 / NA 86M201I (ATG→ATA) yihFconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/56);  total (30/56)

CCGGAAATTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATGAAC  >  W3110S.gb/3591813‑3591944
                                                                   |                                                                
ccGGAAATTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTAtt                                                               <  1:743193/71‑1 (MQ=255)
      aTTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGAt                                                         <  1:1029577/71‑1 (MQ=255)
      aTTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGAt                                                         <  1:3591920/71‑1 (MQ=255)
      aTTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGAt                                                         <  1:4110309/71‑1 (MQ=255)
      aTTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGAt                                                         <  1:2598816/71‑1 (MQ=255)
      aTTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGAt                                                         <  1:1979359/71‑1 (MQ=255)
      aTTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGAt                                                         <  1:1124301/71‑1 (MQ=255)
      aTTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGAt                                                         <  1:2593416/71‑1 (MQ=255)
      aTTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGAt                                                         <  1:2510286/71‑1 (MQ=255)
        ttcttttcttCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATa                                                        >  1:4139688/1‑70 (MQ=255)
         tcttttcttCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAAt                                                      >  1:4563697/1‑71 (MQ=255)
         tcttttcttCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAAt                                                      >  1:3444099/1‑71 (MQ=255)
                  ctAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAAc                                              <  1:2509166/70‑1 (MQ=255)
                  ctAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAAc                                              <  1:1339128/70‑1 (MQ=255)
                  ctAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAAc                                              <  1:3171986/70‑1 (MQ=255)
                  ctAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCAGTTACTTTGTTTATTGGTGATAATTGCAGAAc                                              <  1:3297410/70‑1 (MQ=255)
                     aTCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACaa                                            <  1:2441236/69‑1 (MQ=255)
                     aTCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAata                                          <  1:3320279/71‑1 (MQ=255)
                     aTCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAata                                          >  1:2921164/1‑71 (MQ=255)
                     aTCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAat                                           <  1:1522331/70‑1 (MQ=255)
                     aTCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAat                                           <  1:1356725/70‑1 (MQ=255)
                     aTCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAat                                           <  1:1097448/70‑1 (MQ=255)
                     aTCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAat                                           <  1:1090148/70‑1 (MQ=255)
                       cgcgCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATc                                        >  1:1438903/1‑71 (MQ=255)
                       cgcgCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATc                                        >  1:1912007/1‑71 (MQ=255)
                        gcgcCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCt                                       >  1:314262/1‑71 (MQ=255)
                          gcCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTc                                     <  1:1853961/71‑1 (MQ=255)
                             agagAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGAc                                  <  1:3105440/71‑1 (MQ=255)
                             agagAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGAc                                  <  1:4290787/71‑1 (MQ=255)
                             agagAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGAc                                  <  1:4485671/71‑1 (MQ=255)
                             agagAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGAc                                  <  1:2524182/71‑1 (MQ=255)
                             agagAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGAc                                  <  1:824213/71‑1 (MQ=255)
                             agagAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGAc                                  <  1:1037639/71‑1 (MQ=255)
                               agaATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATATTCGACtt                                >  1:482509/1‑71 (MQ=255)
                                gaATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTgg                                                             >  1:2253597/1‑41 (MQ=255)
                                gaATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACttt                               >  1:996733/1‑71 (MQ=255)
                                gaATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACttt                               >  1:1058403/1‑71 (MQ=255)
                                gaATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACttt                               <  1:1333188/71‑1 (MQ=255)
                                gaATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACt                                 >  1:2513390/1‑69 (MQ=255)
                                   tCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGcc                            >  1:4303566/1‑71 (MQ=255)
                                   tCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGcc                            >  1:2954895/1‑71 (MQ=255)
                                     aaTGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCtt                          <  1:2345024/71‑1 (MQ=255)
                                       tGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATaa                                                       <  1:4400662/40‑1 (MQ=255)
                                       tGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATaa                                                       <  1:4144280/40‑1 (MQ=255)
                                       tGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTc                         >  1:989861/1‑70 (MQ=255)
                                       tGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTc                         >  1:3259508/1‑70 (MQ=255)
                                         gTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGAt                                                         <  1:1237271/36‑1 (MQ=255)
                                         gTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAat                                           <  1:556982/50‑1 (MQ=255)
                                         gTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAat                                           <  1:518848/50‑1 (MQ=255)
                                         gTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAat                                           <  1:922826/50‑1 (MQ=255)
                                         gTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAat                                           <  1:408470/50‑1 (MQ=255)
                                         gTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACt                                 >  1:3214236/1‑60 (MQ=255)
                                         gTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACt                                 >  1:3019640/1‑60 (MQ=255)
                                         gTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCaa                       >  1:2529013/1‑70 (MQ=255)
                                         gTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCaa                       >  1:1801282/1‑70 (MQ=255)
                                         gTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCaa                       <  1:3469238/70‑1 (MQ=255)
                                           aaaaCTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCaa                       <  1:1312861/68‑1 (MQ=255)
                                            aaaCTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATGTTCGACTTTGCCTTCAATATc                   >  1:121027/1‑71 (MQ=255)
                                            aaaCTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTGGACTTTGCCTTCAATATc                   <  1:1203015/71‑1 (MQ=255)
                                            aaaCTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGcc                            >  1:1575027/1‑62 (MQ=255)
                                            aaaCTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATc                   <  1:3633012/71‑1 (MQ=255)
                                            aaaCTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATc                   <  1:3969389/71‑1 (MQ=255)
                                              aCTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATc                   >  1:1215586/1‑69 (MQ=255)
                                              aCTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATc                   >  1:2257825/1‑69 (MQ=255)
                                                  tttGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGt              <  1:1089895/70‑1 (MQ=255)
                                                      ccGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGAc         <  1:2712399/71‑1 (MQ=255)
                                                      ccGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGAc         <  1:2653257/71‑1 (MQ=255)
                                                      ccGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGAc         <  1:1547366/71‑1 (MQ=255)
                                                        gTTTCTTTGTTTATTGGTGATAATTGCAGTACAATATCTTCGACTTTGc                             <  1:1974187/49‑1 (MQ=38)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCaa                       >  1:467870/1‑52 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCaa                       >  1:2681950/1‑52 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACaa       >  1:3441235/1‑68 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAAtt     >  1:4557030/1‑69 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:1096296/70‑1 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:2398358/70‑1 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:4404938/70‑1 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:3949924/70‑1 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:361958/70‑1 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:1460512/70‑1 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:3306182/70‑1 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:1540332/70‑1 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:3023563/70‑1 (MQ=255)
                                                           aCTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     >  1:1933942/1‑70 (MQ=255)
                                                            cTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATGa    <  1:3513151/70‑1 (MQ=255)
                                                             tttGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTc                         <  1:995136/48‑1 (MQ=255)
                                                              ttGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATGAAc  >  1:4354859/1‑70 (MQ=255)
                                                                   |                                                                
CCGGAAATTTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATGAAC  >  W3110S.gb/3591813‑3591944

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