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 1,677,332 C→A 38.7% V73V (GTG→GTT)  ndk ← multifunctional nucleoside diphosphate kinase, apyrimidinic endonuclease, and 3'‑phosphodiesterase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,677,3320CA38.7% 79.6 / 78.7 98V73V (GTG→GTT) ndkmultifunctional nucleoside diphosphate kinase, apyrimidinic endonuclease, and 3'‑phosphodiesterase
Reads supporting (aligned to +/- strand):  ref base C (26/34);  new base A (22/16);  total (48/50)
Fisher's exact test for biased strand distribution p-value = 2.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

GGATTGGTCGCGCCCAGCAGATCGCGGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTCCATCGTG  >  minE/1677267‑1677391
                                                                 |                                                           
ggATTGGTCGCGCCCAGCAGATCGCGGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACg                                                          <  1:3366529/69‑1 (MQ=255)
ggATTGGTCGCGCCCAGCAGATCGCGGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACg                                                          <  1:1387093/69‑1 (MQ=255)
ggATTGGTCGCGCCCAGCAGATCGCGGTGACGCTGAACGCCGTTTTCACCTTCCAGCACGGAAACCACg                                                          <  1:1920302/69‑1 (MQ=255)
     ggTCGCGCCCAGCAGATCGCGGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCgg                                                     <  1:1839072/69‑1 (MQ=255)
     ggTCGCGCCCAGCAGATCGCGGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCgg                                                     <  1:1492173/69‑1 (MQ=255)
      gTCGCGCCCAGCAGATCGCGGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCgg                                                     <  1:3312622/68‑1 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCGAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:1683041/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:3354367/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:73166/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:2553414/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:2267659/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:2178319/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:2061394/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:810006/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:904004/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:980430/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:2528038/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:1587276/1‑68 (MQ=255)
                      cgcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAAt                                     >  1:1083017/1‑68 (MQ=255)
                       gcgGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTc                                   <  1:2435394/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACTATCGGGCCAGAAGTCATGAATTc                                   <  1:3041782/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGCTCGGGCCAGAAGTCATGAATTc                                   <  1:3031122/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:2752079/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:2616573/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:2344932/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:2086975/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:1496863/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:1289881/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:543600/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:1768475/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:594060/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:632105/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:843453/69‑1 (MQ=255)
                       gcgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:1679948/69‑1 (MQ=255)
                        cgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:2789974/68‑1 (MQ=255)
                        cgGTGACGCTGAACAGCATTTTCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTc                                   <  1:29244/68‑1 (MQ=255)
                             aCGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAg                             >  1:471833/1‑69 (MQ=255)
                             aCGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAg                             >  1:2840056/1‑69 (MQ=255)
                               gCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGAc                           <  1:3319402/69‑1 (MQ=255)
                               gCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGAc                           <  1:2612174/69‑1 (MQ=255)
                               gCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGAc                           <  1:1408027/69‑1 (MQ=255)
                               gCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGAc                           <  1:298218/69‑1 (MQ=255)
                                          ttttCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAg                   >  1:2580705/1‑66 (MQ=255)
                                          ttttCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:1888597/1‑69 (MQ=255)
                                          ttttCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:1063473/1‑69 (MQ=255)
                                          ttttCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:3228295/1‑69 (MQ=255)
                                          ttttCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:1392250/1‑69 (MQ=255)
                                          ttttCACCTTCCAGCACGGAAACCACGATCGCGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:1892499/1‑69 (MQ=255)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATg                                        >  1:1639416/1‑45 (MQ=255)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCaa                                 >  1:1394146/1‑52 (MQ=255)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGaa                 >  1:3071500/1‑68 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:750239/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:3165620/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:3171707/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:2965126/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:1178728/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:944606/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:3340827/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:158730/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:2735909/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:2731804/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:2694234/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:1917989/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:198181/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:1676670/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:1997996/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:1743617/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:1753476/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATTCAACCAGACCATCAAAGAAc                >  1:2106531/1‑69 (MQ=39)
                                          ttttCACCTTCCAGCACGGAAACAACGATCGGGCCAGAAGTCATGAATACAACCAGACCATCAAAGAAc                >  1:2088350/1‑69 (MQ=255)
                                            ttCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAg                             >  1:675036/1‑54 (MQ=255)
                                            ttCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAg                             >  1:1909228/1‑54 (MQ=255)
                                            ttCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAg                             >  1:1752612/1‑54 (MQ=255)
                                            ttCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAg                             >  1:2159230/1‑54 (MQ=255)
                                            ttCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAg                             >  1:2957229/1‑54 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:612313/68‑1 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:279084/68‑1 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:1578457/68‑1 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:1085080/68‑1 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:1630514/68‑1 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:453677/68‑1 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:1909418/68‑1 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:2977265/68‑1 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:2259250/68‑1 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:225538/68‑1 (MQ=255)
                                                ccTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:3116304/68‑1 (MQ=255)
                                                 cTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGttt           <  1:1074139/67‑1 (MQ=255)
                                                 cTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTc         <  1:3138318/69‑1 (MQ=255)
                                                 cTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTc         <  1:1455161/69‑1 (MQ=255)
                                                 cTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTc         <  1:1656029/69‑1 (MQ=255)
                                                  ttCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTc         <  1:2531597/68‑1 (MQ=255)
                                                        cACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTCCATCgtg  <  1:3153910/69‑1 (MQ=255)
                                                        cACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTCCATCgtg  <  1:149183/69‑1 (MQ=255)
                                                        cACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTCCATCgtg  <  1:156878/69‑1 (MQ=255)
                                                        cACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTCCATCgtg  <  1:3311926/69‑1 (MQ=255)
                                                        cACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTCCATCgtg  <  1:1297739/69‑1 (MQ=255)
                                                        cACGGAAACCACGATCGGGCCAGAGGTCATAAATTCAACCAGACCATCAAAGAACGGTTTTCCATCgtg  <  1:716009/69‑1 (MQ=255)
                                                             aaaCCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTCCATCgtg  <  1:3400386/64‑1 (MQ=255)
                                                                 |                                                           
GGATTGGTCGCGCCCAGCAGATCGCGGTGACGCTGAACGGCGTTTTCACCTTCCAGCACGGAAACCACGATCGGGCCAGAGGTCATGAATTCAACCAGACCATCAAAGAACGGTTTTCCATCGTG  >  minE/1677267‑1677391

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