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 3,332,615 T→A 36.6% intergenic (‑25/+102) yhbE ← / ← rpmA conserved inner membrane protein/50S ribosomal subunit protein L27

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,332,6150TA36.6% 82.6 / 88.6 82intergenic (‑25/+102)yhbE/rpmAconserved inner membrane protein/50S ribosomal subunit protein L27
Reads supporting (aligned to +/- strand):  ref base T (17/35);  new base A (13/17);  total (30/52)
Fisher's exact test for biased strand distribution p-value = 3.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGTGAGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGCCCCGCAACGTGTTGCGG  >  W3110S.gb/3332548‑3332685
                                                                   |                                                                      
tggtgAGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCg                                                                     <  1:547812/71‑1 (MQ=255)
tggtgAGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCg                                                                     <  1:1317925/71‑1 (MQ=255)
tggtgAGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCg                                                                     <  1:719336/71‑1 (MQ=255)
tggtgAGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCg                                                                     <  1:4574511/71‑1 (MQ=255)
  gtgAGCGGCAAAAGAATGACAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGa                                                                   >  1:1406770/1‑71 (MQ=255)
  gtgAGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGa                                                                   >  1:3201096/1‑71 (MQ=255)
  gtgAGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGa                                                                   >  1:696244/1‑71 (MQ=255)
  gtgAGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGa                                                                   <  1:1578816/71‑1 (MQ=255)
   tgAGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGAt                                                                  >  1:2337112/1‑71 (MQ=255)
     aGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:2807692/70‑1 (MQ=255)
       cgcCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAAc                                                              <  1:2556404/71‑1 (MQ=255)
       cgcCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGa                                                                   <  1:182268/66‑1 (MQ=255)
       cgcCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAAc                                                              <  1:809345/71‑1 (MQ=255)
       cgcCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAAc                                                              <  1:3921985/71‑1 (MQ=255)
       cgcCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAAc                                                              <  1:1345360/71‑1 (MQ=255)
          cAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTc                                                           <  1:1087703/71‑1 (MQ=255)
            aaaGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGc                                                         <  1:3371212/71‑1 (MQ=255)
            aaaGAATGCCAATGCCTGCCTGCTACTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCg                                                          >  1:229296/1‑70 (MQ=255)
            aaaGAATGCCAATGCCTGCCTGCGGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCg                                                          >  1:3039334/1‑70 (MQ=255)
             aaGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGCa                                                        >  1:1729581/1‑71 (MQ=255)
             aaGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGCa                                                        >  1:3497329/1‑71 (MQ=255)
                   gccaatgccTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCAcc                                                      <  1:351251/67‑1 (MQ=255)
                   gccaatgccTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCAcc                                                      <  1:2294658/67‑1 (MQ=255)
                    ccaatgccTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACg                                                             <  1:3535090/59‑1 (MQ=255)
                     caatgccTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATgcgc                                                <  1:1014605/71‑1 (MQ=255)
                         gcctgcctGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCg                                                                     >  1:4224311/1‑46 (MQ=255)
                         gcctgcctGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCAtt                                             >  1:647421/1‑70 (MQ=255)
                          cctgcctgCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCAtttt                                           >  1:963354/1‑71 (MQ=255)
                          cctgcctgCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCAtttt                                           <  1:4238000/71‑1 (MQ=255)
                           ctgcctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCAttttt                                          <  1:1141163/71‑1 (MQ=255)
                           ctgcctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCAttttt                                          <  1:1135095/71‑1 (MQ=255)
                           ctgcctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCAttttt                                          <  1:137013/71‑1 (MQ=255)
                            tgcctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCg                                                                     <  1:4017764/43‑1 (MQ=255)
                            tgcctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:1312450/47‑1 (MQ=255)
                            tgcctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:3816281/47‑1 (MQ=255)
                            tgcctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:4495116/47‑1 (MQ=255)
                             gcctgcTGCTTCATACCGTATTCCCTGCAAAGCGAATTTGCGGATTAACGTCGCACCATGCGCATTTTTAc                                        >  1:116755/1‑71 (MQ=255)
                              cctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTg                                                                       >  1:1022968/1‑39 (MQ=255)
                              cctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTaa                                                               >  1:2172559/1‑47 (MQ=255)
                              cctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTaa                                                               >  1:2092266/1‑47 (MQ=255)
                              cctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTaa                                                               >  1:3705881/1‑47 (MQ=255)
                              cctgcTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTaa                                                               >  1:5136627/1‑47 (MQ=255)
                                tgctgcTTCATACCGTATTCCCTGCAAAGCGCATTAGCGGAtt                                                                 <  1:3388967/43‑1 (MQ=255)
                                   tgctTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:2972685/40‑1 (MQ=255)
                                   tgctTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:4610836/40‑1 (MQ=255)
                                   tgctTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:779399/40‑1 (MQ=255)
                                   tgctTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:1189832/40‑1 (MQ=255)
                                   tgctTCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTAc                                        >  1:3058304/1‑65 (MQ=255)
                                    gctTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:606488/39‑1 (MQ=255)
                                    gctTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:722060/39‑1 (MQ=255)
                                    gctTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:2062846/39‑1 (MQ=255)
                                    gctTCATACCGTATTCCCTGCAAAGCGCATTTGCGGAtt                                                                 <  1:4119142/39‑1 (MQ=255)
                                     ctTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTa                                  <  1:359777/69‑1 (MQ=255)
                                     ctTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTa                                  <  1:3869005/69‑1 (MQ=255)
                                      ttCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTaa                                                               >  1:709661/1‑39 (MQ=255)
                                      ttCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTaa                                                               >  1:3562444/1‑39 (MQ=255)
                                      ttCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTaa                                                               >  1:883601/1‑39 (MQ=255)
                                      ttCATACCGTATTCCCTGCAAAGCGCATTAGCGGATTaa                                                               >  1:3840108/1‑39 (MQ=255)
                                        cATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGa                              <  1:679504/70‑1 (MQ=255)
                                        cATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGa                              <  1:4225350/70‑1 (MQ=255)
                                        cATACCGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGa                              <  1:4219449/70‑1 (MQ=255)
                                         aTACCGTATTCCCTGCGAAGCGCATTAGCGGATTAACGTCGc                                                         <  1:3365156/42‑1 (MQ=38)
                                         aTACCGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCg                               <  1:148905/68‑1 (MQ=255)
                                           aCCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATg                           >  1:3867663/1‑70 (MQ=255)
                                            ccGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGt                          <  1:3491888/70‑1 (MQ=255)
                                            ccGTATTCCCTGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATg                           >  1:2137003/1‑69 (MQ=255)
                                             cGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTa                         <  1:401993/70‑1 (MQ=255)
                                              gTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTaaa                       <  1:1909424/71‑1 (MQ=255)
                                                 ttCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGa                              <  1:3513066/61‑1 (MQ=255)
                                                 ttCCCTGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTaaaaa                     <  1:771573/70‑1 (MQ=255)
                                                 ttCCCAGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTaaaaa                     <  1:3499599/70‑1 (MQ=255)
                                                   cccTGCAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGc                   <  1:2054732/70‑1 (MQ=255)
                                                    ccTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCAt                                              >  1:295479/1‑42 (MQ=255)
                                                        cAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCAttttt                                          <  1:2712205/42‑1 (MQ=255)
                                                        cAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTAc                                        >  1:3473727/1‑44 (MQ=255)
                                                        cAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGCCCCGCa             <  1:1258104/71‑1 (MQ=255)
                                                        cAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGCCCCGCa             <  1:2632787/71‑1 (MQ=255)
                                                        cAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGa                              >  1:2445734/1‑54 (MQ=255)
                                                        cAAAGCGCATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGa                              >  1:2541300/1‑54 (MQ=255)
                                                            gcgcATTAGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGcc                  >  1:2569296/1‑62 (MQ=255)
                                                             cgcATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTaaa                       >  1:3660735/1‑56 (MQ=255)
                                                                aTTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGCCCCGCAACGTGTTg     <  1:4350454/71‑1 (MQ=255)
                                                                 tttGCGGATTAACGTCGCACCATGCGCATTTTTACCg                                      <  1:4848718/37‑1 (MQ=255)
                                                                  ttGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTaaaaa                     <  1:1153742/53‑1 (MQ=255)
                                                                   tGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGc                   >  1:1943708/1‑54 (MQ=255)
                                                                   tGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGc                   >  1:845000/1‑54 (MQ=255)
                                                                   tGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGCCCCGCAACGTGTTGCgg  >  1:4349115/1‑71 (MQ=255)
                                                                   |                                                                      
TGGTGAGCGCCAAAAGAATGCCAATGCCTGCCTGCTGCTTCATACCGTATTCCCTGCAAAGCGCATTTGCGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGCCCCGCAACGTGTTGCGG  >  W3110S.gb/3332548‑3332685

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