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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,932,853 C→T 20.9% intergenic (‑224/+72) yqeF ← / ← lysS predicted acyltransferase/lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,932,8530CT20.9% 187.4 / 42.4 86intergenic (‑224/+72)yqeF/lysSpredicted acyltransferase/lysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base C (33/35);  new base T (12/6);  total (45/41)
Fisher's exact test for biased strand distribution p-value = 1.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

ACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGTAATG  >  minE/1932783‑1932923
                                                                      |                                                                      
accaATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTc                                                                        >  1:812170/1‑71 (MQ=255)
accaATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTc                                                                        <  1:2448144/71‑1 (MQ=255)
       gagGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTa                                                                  <  1:1643801/70‑1 (MQ=255)
        agGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAAt                                                                <  1:2856822/71‑1 (MQ=255)
           ggTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTg                                                             <  1:3532330/71‑1 (MQ=255)
            gTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTg                                                             >  1:2455419/1‑70 (MQ=255)
            gTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGt                                                            <  1:1608542/71‑1 (MQ=255)
            gTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTg                                                             <  1:313773/70‑1 (MQ=255)
                 tAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAga                                                         >  1:1583919/1‑69 (MQ=255)
                 tAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTAGTTgat                                                        >  1:1868609/1‑70 (MQ=255)
                   gggCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAg                                                          <  1:2543656/66‑1 (MQ=255)
                      cGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACg                                                  >  1:2459237/1‑71 (MQ=255)
                       gTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAGATGATACGt                                                 >  1:1219921/1‑71 (MQ=255)
                        ttAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAGATGATACGt                                                 <  1:3786335/70‑1 (MQ=255)
                          aaTCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTa                                                           >  1:1242272/1‑58 (MQ=255)
                          aaTCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAGATGATACGtt                                                >  1:3723527/1‑69 (MQ=255)
                          aaTCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAGATGATACGt                                                 >  1:3785992/1‑68 (MQ=255)
                          aaTCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAga                                                         >  1:2962341/1‑60 (MQ=255)
                          aaTCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTc                                               >  1:3181886/1‑70 (MQ=255)
                          aaTCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTc                                               >  1:1922305/1‑70 (MQ=255)
                          aaTCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTc                                               >  1:1938473/1‑70 (MQ=255)
                           aTCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAGATGATACGtt                                                >  1:2855447/1‑68 (MQ=255)
                           aTCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTa                                             <  1:3547361/71‑1 (MQ=255)
                              tcCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGttt                                                                   <  1:3849997/46‑1 (MQ=255)
                              tcCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGttt                                                                   <  1:2929073/46‑1 (MQ=255)
                              tcCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTa                                                           >  1:1726554/1‑54 (MQ=255)
                              tcCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTa                                             >  1:1967370/1‑68 (MQ=255)
                                ccATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTaaaaa                                         >  1:1502357/1‑70 (MQ=255)
                                ccATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTaaaaa                                         >  1:4142141/1‑70 (MQ=255)
                                  aTACTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTa                                                           >  1:3853155/1‑50 (MQ=255)
                                  aTACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGtt                                                >  1:1119201/1‑61 (MQ=255)
                                   tACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTaaaaaaa                                       >  1:2591251/1‑69 (MQ=255)
                                    aCTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAAt                                                                >  1:2952445/1‑43 (MQ=255)
                                     cTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTaa                                                                 <  1:3960081/41‑1 (MQ=255)
                                     cTTAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAgat                                                        >  1:927346/1‑50 (MQ=255)
                                     cTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTa                                                           >  1:1949180/1‑47 (MQ=255)
                                     cTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAgatga                                                      >  1:65429/1‑52 (MQ=255)
                                     cTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATa                                                    >  1:3458563/1‑54 (MQ=255)
                                     cTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATa                                                    >  1:2687407/1‑54 (MQ=255)
                                     cTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAAcccc                                   >  1:1975595/1‑71 (MQ=255)
                                      ttAACCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAGATGATACGt                                                 <  1:1886776/56‑1 (MQ=255)
                                       tAACCTGGTTTATGGTAAATTGCCCTCCATTCTGt                                                                     >  1:2955725/1‑35 (MQ=255)
                                       tAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGa                                 >  1:3468748/1‑71 (MQ=255)
                                        aaCCTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAAt                                                                >  1:3854136/1‑39 (MQ=255)
                                         aCCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGa                                 <  1:999872/69‑1 (MQ=255)
                                          ccTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAGATGATACGTTc                                               <  1:2756562/54‑1 (MQ=255)
                                          ccTGGTTTATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAGATGATACGTTc                                               <  1:2933008/54‑1 (MQ=255)
                                           cTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAgat                                                        <  1:521550/44‑1 (MQ=255)
                                           cTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACAtt                             <  1:2652139/71‑1 (MQ=255)
                                            tGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAgatga                                                      <  1:1499754/45‑1 (MQ=255)
                                            tGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAgat                                                        <  1:3033196/43‑1 (MQ=255)
                                              gTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATa                                                    >  1:877451/1‑45 (MQ=255)
                                              gTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGc                          >  1:3522606/1‑71 (MQ=255)
                                               tttATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAgat                                                        <  1:3568861/40‑1 (MQ=255)
                                                ttATGGTAAATTGCCCTCCATTTTGTTTAATTTGTAgatga                                                      >  1:1228157/1‑41 (MQ=255)
                                                 tATGGTAAATTGCCCTCCATTTTGTTTAATTTGTa                                                           >  1:456676/1‑35 (MQ=255)
                                                 tATGGTAAAATGCCCTCCATTCTGTTTAATTTGTAgat                                                        <  1:1774174/38‑1 (MQ=255)
                                                     gTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGt                    <  1:2850811/70‑1 (MQ=255)
                                                      tAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTa                                             >  1:3013657/1‑44 (MQ=255)
                                                       aaaTTGCCCTCCAATCTGTTTAATTTGTAGATGATACGTTCTa                                             >  1:1384359/1‑43 (MQ=255)
                                                         aTTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAAc                                      <  1:188211/48‑1 (MQ=255)
                                                              ccTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATa          <  1:3272443/71‑1 (MQ=255)
                                                               cTCCATTCTGTTTAATTTGTAGATGATACGTTCTaaaaaaa                                       >  1:364080/1‑41 (MQ=255)
                                                               cTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACAt                              >  1:2159959/1‑50 (MQ=255)
                                                               cTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAg              <  1:2843310/66‑1 (MQ=255)
                                                               cTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGc             >  1:1496202/1‑67 (MQ=255)
                                                               cTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATa          <  1:2145994/70‑1 (MQ=255)
                                                                tCCATTCTGTTTAATTTGTAGATGATACGTTCTaaaaa                                         <  1:248583/38‑1 (MQ=255)
                                                                 ccATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTg                           >  1:3609514/1‑51 (MQ=255)
                                                                 ccATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCa            >  1:3248876/1‑66 (MQ=255)
                                                                 ccATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCa            >  1:2870567/1‑66 (MQ=255)
                                                                 ccATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACg       >  1:1477265/1‑71 (MQ=255)
                                                                  cATTCTGTTTAATTTGTAGATGATACGTTCTaaaaaaa                                       >  1:3097573/1‑38 (MQ=255)
                                                                  cATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACg       <  1:940060/70‑1 (MQ=255)
                                                                  cATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACg       >  1:3331982/1‑70 (MQ=255)
                                                                  cATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGt      <  1:3700661/71‑1 (MQ=255)
                                                                  cATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGt      <  1:2304615/71‑1 (MQ=255)
                                                                  cATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGt      <  1:2144871/71‑1 (MQ=255)
                                                                  cATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGt      <  1:678605/71‑1 (MQ=255)
                                                                  cATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGt      <  1:3114561/71‑1 (MQ=255)
                                                                  cATTCTGTTTAATTTGTAGATGATACGTTCT‑AAAAAACCCCGACATTTg                           <  1:899316/49‑1 (MQ=255)
                                                                   aTTCTGTTTAATTTGTAGATGATACGTTCT‑AAAAAACCCCGACATTTg                           <  1:2289815/48‑1 (MQ=255)
                                                                    ttCTGTTTAATTTGTAGATGATACGTTCTaaaaaa                                        <  1:1000555/35‑1 (MQ=255)
                                                                    ttCTGTTTAATTTGTAGATGATACGTTCTaaaaaa                                        <  1:1324807/35‑1 (MQ=255)
                                                                    ttCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGAc                                <  1:4135418/43‑1 (MQ=255)
                                                                    ttCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGt      <  1:3611023/69‑1 (MQ=255)
                                                                    ttCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGt      <  1:2293235/69‑1 (MQ=255)
                                                                    ttCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGt      <  1:3719499/69‑1 (MQ=255)
                                                                      cTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGa                                 >  1:1260391/1‑40 (MQ=255)
                                                                      cTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACa                               >  1:2168580/1‑42 (MQ=255)
                                                                      cTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACa                               >  1:2620867/1‑42 (MQ=255)
                                                                      cTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACa                               >  1:1150473/1‑42 (MQ=255)
                                                                      cTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGTaa    >  1:1908374/1‑69 (MQ=255)
                                                                      cTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGTAATg  >  1:4119306/1‑71 (MQ=255)
                                                                      cTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGTAATg  >  1:1120356/1‑71 (MQ=255)
                                                                      cTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGTAATg  >  1:3507918/1‑71 (MQ=255)
                                                                      |                                                                      
ACCAATAGAGGGGTAGATAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAAATTGCCCTCCATTCTGTTTAATTTGTAGATGATACGTTCTAAAAAAACCCCGACATTTGCCGGGGTTGTGAGCATAACGTAATG  >  minE/1932783‑1932923

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