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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,630,965 G→A 26.0% A60A (GCG→GCA)  livH → leucine/isoleucine/valine transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,630,9650GA26.0% 105.5 / 31.3 88A60A (GCG→GCA) livHleucine/isoleucine/valine transporter subunit
Reads supporting (aligned to +/- strand):  ref base G (28/37);  new base A (15/8);  total (43/45)
Fisher's exact test for biased strand distribution p-value = 9.03e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCAACTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGATTCGTCGGCGCAAT  >  minE/2630900‑2631027
                                                                 |                                                              
aTCAACTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtg                                                             >  1:2593643/1‑69 (MQ=255)
aTCAACTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtg                                                             >  1:2938531/1‑69 (MQ=255)
aTCAACTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtg                                                             >  1:981489/1‑69 (MQ=255)
aTCAACTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtg                                                             >  1:2995093/1‑69 (MQ=255)
aTCAACTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtg                                                             >  1:3097999/1‑69 (MQ=255)
aTCAACTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtg                                                             >  1:734193/1‑69 (MQ=255)
aTCAACTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtg                                                             >  1:339037/1‑69 (MQ=255)
aTCAACTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtg                                                             >  1:1508125/1‑69 (MQ=255)
  cAACTTCGCCCACGGCGAGGTTTACATGATTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACtgat                                                           <  1:1044161/69‑1 (MQ=255)
  cAACTTCGCCCACGGCGAGGTTTACATGATTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACtgat                                                           <  1:2394591/69‑1 (MQ=255)
  cAACTTCGCCCACGGCGAGGTTTACATGATTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACtgat                                                           <  1:2126883/69‑1 (MQ=255)
  cAACTTCGCCCACGGCGAGGTTTACATGATTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACtgat                                                           <  1:3049012/69‑1 (MQ=255)
  cAACTTCGCCCACGGCGAGGTTTACATGATTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACtgat                                                           <  1:1637790/69‑1 (MQ=255)
  cAACTTCGCCCACGGCGAGGTTTACATGATTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACtgat                                                           <  1:1184540/69‑1 (MQ=255)
   aaCTTCGCCCACGGCGAGGTTTACATGATTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACtgat                                                           <  1:2907083/68‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:1927477/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:2303592/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:2151821/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:109306/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:992384/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:2409169/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:2482393/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:249750/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:2617699/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:2621891/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:275136/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:3267197/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:128597/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:2662906/69‑1 (MQ=255)
     cTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGGCTCATTTATGATCATCGCCGAGCtgatgat                                                        <  1:2502932/69‑1 (MQ=255)
      ttCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:2679447/68‑1 (MQ=255)
      ttCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:398444/68‑1 (MQ=255)
      ttCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:3202010/68‑1 (MQ=255)
      ttCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:1363191/68‑1 (MQ=255)
             aCGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCtgatgat                                                        <  1:1273050/61‑1 (MQ=255)
              cGGCGAGGTTTACATGATTGGCAGCTACGGCTCCTTTATGATCATCGCCGCACtgat                                                           <  1:875508/57‑1 (MQ=255)
               ggCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCt                                                              >  1:2251998/1‑53 (MQ=255)
               ggCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCt                                                              >  1:289466/1‑53 (MQ=255)
               ggCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCt                                                              >  1:2360659/1‑53 (MQ=255)
               ggCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCt                                                              >  1:3127952/1‑53 (MQ=255)
               ggCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCt                                                              >  1:1837532/1‑53 (MQ=255)
               ggCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCt                                                              >  1:3333336/1‑53 (MQ=255)
               ggCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCAtt                                              <  1:928406/69‑1 (MQ=255)
               ggCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCAtt                                              <  1:3072131/69‑1 (MQ=255)
               ggCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCAtt                                              <  1:3108210/69‑1 (MQ=255)
               ggCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCAtt                                              <  1:1046061/69‑1 (MQ=255)
                  gaagTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:3253309/66‑1 (MQ=255)
                  gAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGTATTGAt                                           <  1:4082/69‑1 (MQ=255)
                  gAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:1051147/69‑1 (MQ=255)
                  gAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:235270/69‑1 (MQ=255)
                  gAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:98237/69‑1 (MQ=255)
                  gAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:3183665/69‑1 (MQ=255)
                  gAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:3167934/69‑1 (MQ=255)
                  gAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:2078186/69‑1 (MQ=255)
                  gAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:3152258/69‑1 (MQ=255)
                  gAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:519569/69‑1 (MQ=255)
                  gAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:1660335/69‑1 (MQ=255)
                   aGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGAt                                           <  1:2021063/68‑1 (MQ=255)
                        tataTGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGATACCggc                                     >  1:3087002/1‑69 (MQ=255)
                        tataTGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGATACCggc                                     >  1:1876237/1‑69 (MQ=255)
                        tataTGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGATACCggc                                     >  1:1905824/1‑69 (MQ=255)
                        tataTGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGATACCggc                                     >  1:779191/1‑69 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTTATACCggct                                    >  1:2720586/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATa                                          >  1:1186972/1‑58 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:1611945/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:2631331/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:567453/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:600447/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:1142270/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:1630013/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:1722104/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:3132894/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:3113535/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:286924/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTGATGATGCTGGGCATTGATACCggct                                    >  1:21452/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGATCATCGCCGCACTAATGATGCTGGGCATTGATACCggct                                    >  1:1433893/1‑64 (MQ=255)
                              aTTGGCAGCTACGTCTCCTTTATGAACATCGCCGCACTGATGATGCTGGGCATTGATACCggc                                     >  1:1326340/1‑63 (MQ=255)
                                  gCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCAtt                                              <  1:690985/50‑1 (MQ=255)
                                              cATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGAt               >  1:645766/1‑69 (MQ=255)
                                              cATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGAt               >  1:2077674/1‑69 (MQ=255)
                                              cATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGAt               >  1:2969840/1‑69 (MQ=255)
                                                           cgccgcGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGATTCGTCGGCGCAAt  >  1:995936/1‑69 (MQ=255)
                                                           cgccgcGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGATTCGTCGGCGCAAt  >  1:2338558/1‑69 (MQ=255)
                                                           cgccgcGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGATTCGTCGGCGCAAt  >  1:1261152/1‑69 (MQ=255)
                                                           cgccgcGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGATTCGTCGGCGCAAt  >  1:707327/1‑69 (MQ=255)
                                                           cgccgcGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGATTCGTCGGCGCAAt  >  1:631153/1‑69 (MQ=255)
                                                           cgccgcGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGATTCGTCGGCGCAAt  >  1:3421576/1‑69 (MQ=255)
                                                           cgccgcGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGATTCGTAGGCGCAAt  >  1:1971855/1‑69 (MQ=255)
                                                                 |                                                              
ATCAACTTCGCCCACGGCGAGGTTTATATGATTGGCAGCTACGTCTCATTTATGATCATCGCCGCGCTGATGATGATGGGCATTGATACCGGCTGGCTGCTGGTAGCTGCGGGATTCGTCGGCGCAAT  >  minE/2630900‑2631027

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