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 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,163,647 T→A 9.4% N328I (AAC→ATC)  parC ← DNA topoisomerase IV, subunit A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,163,6470TA 9.4% 139.4 / 7.3 53N328I (AAC→ATC) parCDNA topoisomerase IV, subunit A
Reads supporting (aligned to +/- strand):  ref base T (28/20);  new base A (2/3);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 6.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.25e-01

AGCCATTCGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATCCA  >  W3110S.gb/3163578‑3163713
                                                                     |                                                                  
aGCCATTCGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGtt                                                                   <  1:240062/71‑1 (MQ=255)
aGCCATTCGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGtt                                                                   <  1:3572971/71‑1 (MQ=255)
aGCCATTCGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGtt                                                                   <  1:2111358/71‑1 (MQ=255)
       cGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTaa                                                                 >  1:1741878/1‑66 (MQ=255)
               aTTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATAc                                                              <  1:603657/61‑1 (MQ=255)
               aTTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATAc                                                              <  1:3132098/61‑1 (MQ=255)
                 ttCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCtttt                                                  >  1:3940733/1‑71 (MQ=255)
                   ccAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTc                                                 <  1:2948356/70‑1 (MQ=255)
                   ccAGCAAGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTc                                                 >  1:601052/1‑70 (MQ=255)
                      gcagGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTaa                                                                 >  1:1217351/1‑51 (MQ=255)
                          gTTTTTCACCGCCTGACGACCATCCAGACCGATCATATTAAGGTTaa                                                                 <  1:3279923/47‑1 (MQ=255)
                            ttttCACCGCCGGACGACCATCCAGACCGATCATATTAAGGtt                                                                   <  1:3521735/43‑1 (MQ=255)
                             tttCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGa                                                            >  1:4230556/1‑49 (MQ=255)
                              ttCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCggtgg                                      >  1:3869093/1‑70 (MQ=255)
                                  ccgccgGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCg                                 <  1:1345291/71‑1 (MQ=255)
                                    gccgGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAg                                   <  1:1030178/67‑1 (MQ=255)
                                       ggACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAagag                            >  1:1887595/1‑71 (MQ=255)
                                       ggACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAagag                            >  1:1734348/1‑71 (MQ=255)
                                        gacgacCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTc                                                 <  1:2321597/49‑1 (MQ=255)
                                        gacgacCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAgg                           <  1:2907652/71‑1 (MQ=255)
                                        gacgacCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAgg                           <  1:3476689/71‑1 (MQ=255)
                                        gacgacCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAgg                           <  1:4614939/71‑1 (MQ=255)
                                          cgacCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAggtg                         <  1:2494672/71‑1 (MQ=255)
                                             ccATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCgg                                         >  1:2130404/1‑52 (MQ=255)
                                              cATCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAGATCgg                                         <  1:2896073/51‑1 (MQ=255)
                                               aTCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGAt                                            <  1:1793697/47‑1 (MQ=255)
                                               aTCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGAt                                            <  1:2030519/47‑1 (MQ=255)
                                                tCCAGACCGATCATATTAAGGTTAATACGATAGctc                                                      <  1:1721569/36‑1 (MQ=255)
                                                 ccAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcat                   >  1:4514695/1‑70 (MQ=255)
                                                  cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCa                                               >  1:2060961/1‑41 (MQ=255)
                                                  cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCa                                               >  1:3429944/1‑41 (MQ=255)
                                                  cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAggt                          >  1:667994/1‑62 (MQ=255)
                                                  cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcatca                 >  1:1339804/1‑71 (MQ=255)
                                                  cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcatca                 >  1:3458393/1‑71 (MQ=255)
                                                  cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcatca                 >  1:196477/1‑71 (MQ=255)
                                                  cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcatc                  <  1:2664572/70‑1 (MQ=255)
                                                  cAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcatc                  <  1:780806/70‑1 (MQ=255)
                                                   aGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               <  1:2920888/56‑1 (MQ=255)
                                                      ccGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               >  1:2273836/1‑53 (MQ=255)
                                                      ccGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGtt                      >  1:171737/1‑62 (MQ=255)
                                                       cGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCt              >  1:517920/1‑69 (MQ=255)
                                                         aTCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAg                                   <  1:2729506/46‑1 (MQ=255)
                                                         aTCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATc          <  1:255075/71‑1 (MQ=255)
                                                         aTCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATc          <  1:1264329/71‑1 (MQ=255)
                                                         aTCATATTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAgg                           >  1:4392046/1‑54 (MQ=255)
                                                          tCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATc          >  1:4479026/1‑70 (MQ=255)
                                                           cATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCAc                >  1:792141/1‑63 (MQ=255)
                                                           cATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCAc                >  1:2066141/1‑63 (MQ=255)
                                                           cATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTg             >  1:4427880/1‑66 (MQ=255)
                                                           cATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTg             >  1:2561815/1‑66 (MQ=255)
                                                           cATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTg             >  1:255050/1‑66 (MQ=255)
                                                           cATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCa        >  1:4432024/1‑71 (MQ=255)
                                                            atatTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCa        >  1:2082587/1‑70 (MQ=255)
                                                                 aaGGTTAATACGATAGCTCTTTTCCAGATCggtgg                                      >  1:2232639/1‑35 (MQ=255)
                                                                 aaGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATCCa  >  1:3793510/1‑71 (MQ=255)
                                                                    gTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCg                                 <  1:1164410/37‑1 (MQ=255)
                                                                    gTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTg             <  1:2570382/57‑1 (MQ=255)
                                                                     ttAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAag                              <  1:529742/39‑1 (MQ=255)
                                                                     |                                                                  
AGCCATTCGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATCCA  >  W3110S.gb/3163578‑3163713

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