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 3,163,647 T→A 35.7% 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.gb3,163,6470TA35.7% 67.8 / 74.7 70N328I (AAC→ATC) parCDNA topoisomerase IV, subunit A
Reads supporting (aligned to +/- strand):  ref base T (32/13);  new base A (10/15);  total (42/28)
Fisher's exact test for biased strand distribution p-value = 2.09e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01

CATTCGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATCCA  >  W3110S.gb/3163581‑3163713
                                                                  |                                                                  
cATTCGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTaa                                                                 <  1:2542209/70‑1 (MQ=255)
    cGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGa                                                            >  1:1106550/1‑71 (MQ=255)
    cGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGa                                                            >  1:2446128/1‑71 (MQ=255)
    cGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGa                                                            >  1:152992/1‑71 (MQ=255)
    cGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAATACGa                                                            >  1:2428/1‑71 (MQ=255)
     ggAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGa                                                            <  1:153936/70‑1 (MQ=255)
     ggAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGa                                                            <  1:548762/70‑1 (MQ=255)
     ggAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGa                                                            <  1:682503/70‑1 (MQ=255)
     ggAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGa                                                            <  1:3269505/70‑1 (MQ=255)
        gagGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGc                                                        >  1:2574068/1‑71 (MQ=255)
           gATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAATACGATAGctct                                                     >  1:1532457/1‑71 (MQ=255)
           gATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAATACGATAGctct                                                     >  1:2375115/1‑71 (MQ=255)
             tttCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATa                                                               >  1:435637/1‑59 (MQ=255)
               tCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTc                                                 >  1:3437433/1‑71 (MQ=255)
                  agcagGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAg                                              <  1:3472445/71‑1 (MQ=255)
                     agGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAATACGATAGctc                                                      <  1:1561771/60‑1 (MQ=255)
                       gTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATAc                                                              <  1:2462114/50‑1 (MQ=255)
                       gTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCtttt                                                  <  1:1500088/62‑1 (MQ=255)
                       gTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCtttt                                                  <  1:3634170/62‑1 (MQ=255)
                        tttttCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAg                                              <  1:3255308/65‑1 (MQ=255)
                         ttttCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTaa                                                                 >  1:2906306/1‑45 (MQ=255)
                         ttttCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTaa                                                                 >  1:3980229/1‑45 (MQ=255)
                         ttttCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATa                                                          >  1:3469424/1‑52 (MQ=255)
                         ttttCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAg                                                         >  1:3722742/1‑53 (MQ=255)
                         ttttCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAATACGa                                                            >  1:3619305/1‑50 (MQ=255)
                         ttttCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAATACGa                                                            >  1:374707/1‑50 (MQ=255)
                            tCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAAt                                                                <  1:3255752/43‑1 (MQ=255)
                            tCACCGCCGGACGACCATCCAGACCGATCATATTAAGGATAAt                                                                <  1:668254/43‑1 (MQ=255)
                                     gacgacCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTACAGATCGGTGGTAGCGAAGAgg                           <  1:3212287/71‑1 (MQ=255)
                                     gacgacCATCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAgg                           <  1:345917/71‑1 (MQ=255)
                                       cgacCATCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAggtg                         <  1:3054557/71‑1 (MQ=255)
                                          ccATCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAagag                            <  1:1450087/65‑1 (MQ=255)
                                          ccATCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAagag                            <  1:3146792/65‑1 (MQ=255)
                                          ccATCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAagag                            <  1:2459712/65‑1 (MQ=255)
                                          ccATCCAGACCGATCATATTAAGGATAATACGATACCTCTTTTCCAGATCGGTGGTAGCGAagag                            <  1:683085/65‑1 (MQ=255)
                                            aTCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAggt                          >  1:2765792/1‑65 (MQ=255)
                                            aTCCAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAggt                          >  1:270959/1‑65 (MQ=255)
                                             tCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcat                   >  1:3245768/1‑71 (MQ=255)
                                             tCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcat                   >  1:2482526/1‑71 (MQ=255)
                                             tCCAGACCGATCATATTAAGGATAATACGATAGctc                                                      <  1:1037372/36‑1 (MQ=255)
                                               cAGACCGATCATATTAAGGTTAATACGATAGCTCttt                                                   >  1:883089/1‑37 (MQ=255)
                                               cAGACCGATCATATTAAGGTTAATACGATAGCTCttt                                                   >  1:3163571/1‑37 (MQ=255)
                                               cAGACCGATCATATTAAGGTTAATACGATAGCTCttt                                                   >  1:1615432/1‑37 (MQ=255)
                                               cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcatca                 >  1:3678862/1‑71 (MQ=255)
                                               cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcatca                 >  1:157286/1‑71 (MQ=255)
                                               cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcatca                 >  1:3707009/1‑71 (MQ=255)
                                               cAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTtcatca                 >  1:2510182/1‑71 (MQ=255)
                                               cAGACCGATCATATTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               <  1:1930854/57‑1 (MQ=255)
                                                  aCCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               >  1:2996999/1‑54 (MQ=255)
                                                  aCCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               >  1:2312212/1‑54 (MQ=255)
                                                  aCCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               >  1:3049681/1‑54 (MQ=255)
                                                  aCCGATCATATTAAGGTTAATACGATAGCTCTTTTACAGATCGGTGGTAGCGaa                               >  1:2246092/1‑54 (MQ=255)
                                                   ccGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAggtggt                       >  1:3831786/1‑61 (MQ=255)
                                                   ccGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCt              >  1:2016900/1‑70 (MQ=255)
                                                       tCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCggt                                        <  1:3398175/40‑1 (MQ=255)
                                                         atatTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCa        >  1:1444053/1‑70 (MQ=255)
                                                         atatTAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCa        >  1:2434355/1‑70 (MQ=255)
                                                            ttAAGGTTAATACGATAGCTCTTTTCCAGATCggt                                        >  1:509646/1‑35 (MQ=255)
                                                            ttAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               >  1:2026637/1‑44 (MQ=255)
                                                            ttAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               <  1:3633197/44‑1 (MQ=255)
                                                            ttAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               >  1:492480/1‑44 (MQ=255)
                                                            ttAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               >  1:3889742/1‑44 (MQ=255)
                                                            ttAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGaa                               <  1:3749875/44‑1 (MQ=255)
                                                            ttAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATc    >  1:3892844/1‑71 (MQ=255)
                                                            ttAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATc    >  1:2794102/1‑71 (MQ=255)
                                                            ttAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATc    >  1:3029823/1‑71 (MQ=255)
                                                            ttAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAag                              <  1:3793864/45‑1 (MQ=255)
                                                            ttAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAag                              <  1:3720985/45‑1 (MQ=255)
                                                            ttAAGGATAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAag                              <  1:237800/45‑1 (MQ=255)
                                                               aGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATCCa  >  1:497043/1‑70 (MQ=255)
                                                                  ttAATACGATAGCTCTTTTCCAGATCGGTGGTAGCg                                 <  1:2389516/36‑1 (MQ=255)
                                                                  |                                                                  
CATTCGGAGAGGATTTCCAGCAGGTTTTTCACCGCCGGACGACCATCCAGACCGATCATATTAAGGTTAATACGATAGCTCTTTTCCAGATCGGTGGTAGCGAAGAGGTGGTTCATCACCTGATCCATATCCA  >  W3110S.gb/3163581‑3163713

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