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 2,218,928 T→C 10.5% I243I (ATT→ATC)  mlrA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,218,9280TC10.5% 236.6 / 17.7 86I243I (ATT→ATC) mlrADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (43/34);  new base C (5/4);  total (48/38)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

GAACCTCCGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCATTATGCG  >  W3110S.gb/2218858‑2218995
                                                                      |                                                                   
gAACCTCCGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCAtt                                                                     >  1:41772/1‑71 (MQ=255)
      ccGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:882347/1‑71 (MQ=255)
      ccGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:3274430/1‑71 (MQ=255)
      ccGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:4531461/1‑71 (MQ=255)
      ccGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:4981473/1‑71 (MQ=255)
      ccGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:4975629/1‑71 (MQ=255)
      ccGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:245237/1‑71 (MQ=255)
       cGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTaa                                                                  >  1:2230111/1‑67 (MQ=255)
       cGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTaa                                                                  >  1:3599700/1‑67 (MQ=255)
       cGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATg                                                                <  1:4866047/69‑1 (MQ=255)
       cGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGAt                                                              <  1:2439964/71‑1 (MQ=255)
       cGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGAt                                                              <  1:4435733/71‑1 (MQ=255)
       cGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGAt                                                              <  1:2215045/71‑1 (MQ=255)
        gCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGAtt                                                             <  1:69400/71‑1 (MQ=255)
           cAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGt                                                          <  1:1828716/71‑1 (MQ=255)
           cAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGt                                                          <  1:3899111/71‑1 (MQ=255)
           cAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATCTAATGATTCGt                                                          <  1:580078/71‑1 (MQ=255)
                gcagcaACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACa                                                     <  1:2574195/71‑1 (MQ=255)
                gcagcaACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACa                                                     <  1:4336191/71‑1 (MQ=255)
                 cagcaACTCACCAGTTGGCAAGAACTAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACat                                                    <  1:1449553/71‑2 (MQ=255)
                 cagcaACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACa                                                     <  1:4724723/70‑1 (MQ=255)
                     aaCTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATgc                                                <  1:2231381/71‑1 (MQ=255)
                       cTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCg                                                           <  1:2679451/58‑1 (MQ=255)
                       cTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTaa                                                       >  1:2914717/1‑62 (MQ=255)
                        tCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCt                                             >  1:4699089/1‑71 (MQ=255)
                        tCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCt                                             >  1:582838/1‑71 (MQ=255)
                        tCACCAGTTGGAAAGAACAAGGCCATGATATTTTCCCACTCGGCATCTAATGATTCGTTAACAAATGCGCt                                             >  1:2372578/1‑71 (MQ=255)
                         cACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGAGCtt                                            >  1:3821110/1‑71 (MQ=255)
                          aacAGTTGGCAAGAACAAGGCCATGATATTTTCACACTCGGCATTTAATGAt                                                              >  1:1814399/3‑52 (MQ=255)
                          aCCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCtt                                            <  1:3892047/70‑1 (MQ=255)
                          aCCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCtt                                            <  1:769178/70‑1 (MQ=255)
                              gTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTa                                                                   <  1:1855403/43‑1 (MQ=255)
                              gTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGtt                                                         <  1:3689134/53‑1 (MQ=255)
                               ttGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGAtt                                                             <  1:1886418/48‑1 (MQ=255)
                               ttGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACaa                                                    <  1:1594975/57‑1 (MQ=255)
                               ttGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACa                                                     <  1:1962365/56‑1 (MQ=255)
                               ttGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTg                                       >  1:4586865/1‑70 (MQ=255)
                               ttGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTg                                       >  1:493559/1‑70 (MQ=255)
                                tGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATCTAATGATTCGTTAACAAATGCGCTTTACTGTa                                     >  1:4731388/1‑71 (MQ=255)
                                   cAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAAt                                                                 <  1:225127/40‑1 (MQ=255)
                                     aGAACAAGGCCATGATATTTTCCCACTCGGCATTTAAt                                                                 <  1:3293177/38‑1 (MQ=255)
                                     aGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:1028665/1‑40 (MQ=255)
                                     aGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:2171808/1‑40 (MQ=255)
                                     aGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:1240896/1‑40 (MQ=255)
                                     aGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATc                                >  1:2001738/1‑71 (MQ=255)
                                      gAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATcc                               >  1:149409/1‑71 (MQ=255)
                                      gAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATcc                               >  1:3343609/1‑71 (MQ=255)
                                       aaCAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:1386522/1‑38 (MQ=255)
                                       aaCAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:2558069/1‑38 (MQ=255)
                                       aaCAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:1587300/1‑38 (MQ=255)
                                       aaCAAGGCCATGATATTTTCCCACTCGGCATTTAATGa                                                               >  1:1891390/1‑38 (MQ=255)
                                       aaCAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAAc                                                      <  1:7597/47‑1 (MQ=255)
                                        aCAAGGCCATGATATTTTCCCACTCGGCATTTAATg                                                                >  1:3221635/1‑36 (MQ=255)
                                        aCAAGGCCATGATATTTTCCCACTCGGCATTTAATg                                                                >  1:2186803/1‑36 (MQ=255)
                                        aCAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCtt                             <  1:2851586/71‑1 (MQ=255)
                                         cAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCttt                            >  1:2922917/1‑71 (MQ=255)
                                            ggCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGt                         <  1:1587023/71‑1 (MQ=255)
                                            ggCCATGATATTTTCCCACTCGGCATCTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGt                         <  1:4182492/71‑1 (MQ=255)
                                              ccATGATATTTTCCCACTCGGCATTTAATGATTCGTTaa                                                       <  1:2877652/39‑1 (MQ=255)
                                                 tGATATTTTCCCACTCGGCATTTAATGATTCGTTAAc                                                      <  1:429423/37‑1 (MQ=255)
                                                   atatTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATa                  <  1:1011454/71‑1 (MQ=255)
                                                   atatTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATa                  <  1:2044840/71‑1 (MQ=255)
                                                    tatTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCttt                            >  1:695874/1‑60 (MQ=255)
                                                    tatTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACAt                   >  1:4232976/1‑69 (MQ=255)
                                                    tatTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACAt                   >  1:2181137/1‑69 (MQ=255)
                                                    tatTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATa                  <  1:4651388/70‑1 (MQ=255)
                                                    tatTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGATTTACTGTACAAt                                 >  1:1487662/1‑55 (MQ=255)
                                                       tttCCCACTCGGCATCTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGt                         >  1:4837024/1‑60 (MQ=255)
                                                        ttCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAg             >  1:3553381/1‑71 (MQ=255)
                                                        ttCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAg             >  1:3509956/1‑71 (MQ=255)
                                                            cACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATcc                               >  1:1823082/1‑49 (MQ=255)
                                                            cACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATcc                               >  1:1607436/1‑49 (MQ=255)
                                                            cACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCa         >  1:2917339/1‑71 (MQ=255)
                                                            cACTCGGCATCTAATGATTCGTTAACAAATGCGCtt                                            <  1:2176027/36‑1 (MQ=255)
                                                            cACTCGGCATCTAATGATTCGTTAACAAATGCGCtt                                            <  1:3347848/36‑1 (MQ=255)
                                                             aCTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCAt        <  1:120042/71‑1 (MQ=255)
                                                              cTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATaa                 >  1:2412884/1‑61 (MQ=255)
                                                              cTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATaa                 >  1:2311554/1‑61 (MQ=255)
                                                              cTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCAt        <  1:2942335/70‑1 (MQ=255)
                                                              cTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCAt        <  1:1045728/70‑1 (MQ=255)
                                                               tCGGCATCTAATGATTCGTTAACAAATGCGCTTTACTg                                       >  1:4175602/1‑38 (MQ=255)
                                                                cGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCAtt       >  1:5100418/1‑69 (MQ=255)
                                                                 ggCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTaa                      >  1:4920299/1‑53 (MQ=255)
                                                                 ggCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCATTa      <  1:3209316/69‑1 (MQ=255)
                                                                 ggCATCTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCATTa      >  1:1452570/1‑69 (MQ=255)
                                                                    aTTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCATTATgcg  >  1:3431804/1‑70 (MQ=255)
                                                                    aTTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCATTATgcg  >  1:190838/1‑70 (MQ=255)
                                                                     tttAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCAt        <  1:2920857/63‑1 (MQ=255)
                                                                      |                                                                   
GAACCTCCGCCCAACAGCAGCAACTCACCAGTTGGCAAGAACAAGGCCATGATATTTTCCCACTCGGCATTTAATGATTCGTTAACAAATGCGCTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCATTATGCG  >  W3110S.gb/2218858‑2218995

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