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
A2 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 597,552 C→T 54.2% intergenic (+133/‑106) serS → / → dmsA seryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine/dimethyl sulfoxide reductase, anaerobic, subunit A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE597,5520CT54.2% 19.0 / 156.1 107intergenic (+133/‑106)serS/dmsAseryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine/dimethyl sulfoxide reductase, anaerobic, subunit A
Reads supporting (aligned to +/- strand):  ref base C (28/21);  new base T (32/26);  total (60/47)
Fisher's exact test for biased strand distribution p-value = 8.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

Only 100 of 107 total aligned reads displayed.

TTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTT  >  minE/597491‑597616
                                                             |                                                                
ttACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTc                                                         >  1:1301658/1‑71 (MQ=255)
          cTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTaa                                                                <  1:3967523/54‑1 (MQ=255)
          cTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTaa                                                                <  1:615085/54‑1 (MQ=255)
          cTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTaa                                                                <  1:1192724/54‑1 (MQ=255)
          cTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTaa                                                                <  1:3440152/54‑1 (MQ=255)
          cTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATAc                                                >  1:3828058/1‑70 (MQ=255)
          cTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATAc                                                >  1:1576603/1‑70 (MQ=255)
           ttACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGAt                                                      <  1:1051757/63‑1 (MQ=255)
           ttACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGAt                                                      <  1:3094063/63‑1 (MQ=255)
           ttACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGAt                                                      <  1:486591/63‑1 (MQ=255)
            tACACGTAATACTACTTTCGAGTGAAAATCTCCCTATCTCTTTGATTTTCAAATTATTCg                                                        >  1:3705342/1‑60 (MQ=255)
            tACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAat                                                              >  1:341287/1‑54 (MQ=255)
            tACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAat                                                              >  1:3774044/1‑54 (MQ=255)
            tACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAat                                                              >  1:181407/1‑54 (MQ=255)
              cacGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGcc                                           <  1:3259952/71‑1 (MQ=255)
                cGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCt                                          >  1:1718881/1‑70 (MQ=255)
                cGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCt                                          >  1:1713950/1‑70 (MQ=255)
                cGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCt                                          >  1:671155/1‑70 (MQ=255)
                cGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCta                                         <  1:3648576/71‑1 (MQ=255)
                cGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCt                                          <  1:1012861/70‑1 (MQ=255)
                 gTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCta                                         <  1:3368462/70‑1 (MQ=255)
                  tAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtata                                       >  1:3931804/1‑71 (MQ=255)
                  tAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtata                                       <  1:1804619/71‑1 (MQ=255)
                  tAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtata                                       >  1:1430003/1‑71 (MQ=255)
                  tAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtata                                       <  1:778296/71‑1 (MQ=255)
                  tAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtata                                       >  1:2432246/1‑71 (MQ=255)
                    aTACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAatta                                                            >  1:3013140/1‑48 (MQ=255)
                     tactacTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAg                                    >  1:3105364/1‑71 (MQ=255)
                     tactacTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAg                                    >  1:1154346/1‑71 (MQ=255)
                     tactacTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAg                                    >  1:3002513/1‑71 (MQ=255)
                      actactTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGc                                   >  1:1676684/1‑71 (MQ=255)
                      actactTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGc                                   >  1:59412/1‑71 (MQ=255)
                       ctactTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGta                                                   >  1:559673/1‑54 (MQ=255)
                       ctactTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAg                                    >  1:3137747/1‑69 (MQ=255)
                       ctactTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAg                                    >  1:392472/1‑69 (MQ=255)
                       ctactTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAg                                    >  1:360497/1‑69 (MQ=255)
                       ctactTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAg                                    >  1:3705768/1‑69 (MQ=255)
                        tactTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTc                                                         <  1:1879489/47‑1 (MQ=255)
                          ctTTCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAAc                               >  1:3703838/1‑71 (MQ=255)
                           tttCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGAt                                                      <  1:2876836/47‑1 (MQ=255)
                            ttCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTg                             >  1:772451/1‑71 (MQ=255)
                            ttCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGAt                                                      >  1:332498/1‑46 (MQ=255)
                             tCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGc                            >  1:3289988/1‑71 (MQ=255)
                             tCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGc                            >  1:4070835/1‑71 (MQ=255)
                             tCGAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGc                            >  1:1104793/1‑71 (MQ=255)
                               gAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGta                                                   <  1:2002338/46‑1 (MQ=255)
                               gAGTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCt                           <  1:1966942/70‑1 (MQ=255)
                                 gTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCta                          >  1:351611/1‑69 (MQ=255)
                                 gTGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCta                          >  1:585232/1‑69 (MQ=255)
                                  tGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:2944945/60‑1 (MQ=255)
                                  tGAAAATCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:951159/60‑1 (MQ=255)
                                  tGAAAATCTACCTATCTCTTTGATTTTCAAATTATTc                                                         <  1:3580625/37‑1 (MQ=255)
                                   gAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCta                                         <  1:563984/52‑1 (MQ=255)
                                    aaaaTCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCta                                         <  1:2932782/51‑1 (MQ=255)
                                    aaaaTCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCta                                         <  1:1184768/51‑1 (MQ=255)
                                    aaaaTCTACCTATCTCTTTGATTTTCAAATTATTCGa                                                       >  1:398637/1‑37 (MQ=255)
                                    aaaaTCTACCTATCTCTTTGATTTTCAAATTATTCGa                                                       >  1:2588645/1‑37 (MQ=255)
                                    aaaaTCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCt                                          <  1:3817534/50‑1 (MQ=255)
                                     aaaTCTACCTATCTCTTTGATTTTCAAATTATTCGATGt                                                    >  1:3581083/1‑39 (MQ=255)
                                     aaaTCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtata                                       >  1:785034/1‑52 (MQ=255)
                                     aaaTCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtata                                       >  1:2266653/1‑52 (MQ=255)
                                     aaaTCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtata                                       >  1:710492/1‑52 (MQ=255)
                                      aaTCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCtat                                        >  1:914740/1‑50 (MQ=255)
                                      aaTCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAaat                   <  1:1637024/71‑1 (MQ=255)
                                       ctCTTCCGATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCTAACTGc                            <  1:2635503/60‑1 (MQ=255)
                                       ctCTTCCGATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGc                            <  1:3973265/60‑1 (MQ=255)
                                        tCTACCTATCTCTTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAaataa                 >  1:1629118/1‑71 (MQ=255)
                                        tCTACCTATCTCTTTGATTTTTAAATTATTAGATGTATACAAGCCTATATAGCGAACTGCTATAGAaataa                 >  1:1856191/1‑71 (MQ=255)
                                        tCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAaataa                 >  1:2898008/1‑71 (MQ=255)
                                            ccTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGaa                                >  1:1088358/1‑52 (MQ=255)
                                            ccTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGaa                                >  1:3428102/1‑52 (MQ=255)
                                                tctcTTTGATTTTCAAATTATTCGATGTATACAAGCCta                                         <  1:3036661/39‑1 (MQ=255)
                                                tctcTTTGATTTTCAAATTATTCGATGTATACAAGCCta                                         <  1:1500700/39‑1 (MQ=255)
                                                  tctTTGATTTTTAAATTATTCGATTTATACAAGCCTATATAGCGAACTGCTATAGAaataa                 >  1:2584266/1‑61 (MQ=255)
                                                  tctTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAaataa                 >  1:408644/1‑61 (MQ=255)
                                                  tctTTGATTTTCAAATTATTCGATGTATACAAGCCtata                                       >  1:1136856/1‑39 (MQ=255)
                                                  tctTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGaaa                    >  1:4256063/1‑58 (MQ=255)
                                                  tctTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGaaa                    >  1:1455125/1‑58 (MQ=255)
                                                  tctTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGaaa                    >  1:2855699/1‑58 (MQ=255)
                                                  tctTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGaaa                    >  1:2761373/1‑58 (MQ=255)
                                                   ctTTGATTTTTAAATTATTCGATGTATACAAGCCta                                         <  1:739921/36‑1 (MQ=255)
                                                   ctTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:1034942/43‑1 (MQ=255)
                                                   ctTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:1865881/43‑1 (MQ=255)
                                                   ctTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:2914658/43‑1 (MQ=255)
                                                   ctTTGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:1863050/43‑1 (MQ=255)
                                                   ctTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATAc      >  1:26948/1‑71 (MQ=255)
                                                    tttGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACg     >  1:1674747/1‑71 (MQ=255)
                                                    tttGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:2050442/42‑1 (MQ=255)
                                                    tttGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:3441759/42‑1 (MQ=255)
                                                    tttGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:2006073/42‑1 (MQ=255)
                                                     ttGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGaa                                >  1:2075263/1‑43 (MQ=255)
                                                     ttGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGaa                                >  1:1389285/1‑43 (MQ=255)
                                                     ttGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGaa                                >  1:348987/1‑43 (MQ=255)
                                                     ttGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGaa                                >  1:2490297/1‑43 (MQ=255)
                                                     ttGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACgg    >  1:1286606/1‑71 (MQ=255)
                                                      tGATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACgg    <  1:2105002/70‑1 (MQ=255)
                                                       gATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGtt  >  1:2429868/1‑71 (MQ=255)
                                                       gATTTTTAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGt   <  1:2609394/70‑1 (MQ=255)
                                                        aTTTTTAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:352561/38‑1 (MQ=255)
                                                        aTTTTTAAATTATTCGATGTATACAAGCCTATATAGCg                                  <  1:1666385/38‑1 (MQ=255)
                                                             |                                                                
TTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGATTTTCAAATTATTCGATGTATACAAGCCTATATAGCGAACTGCTATAGAAATAATTACACAATACGGTT  >  minE/597491‑597616

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