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 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,591,445 G→A 7.3% T18I (ACA→ATA)  hsdR ← endonuclease R

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,591,4450GA 7.3% 214.6 / 5.7 68T18I (ACA→ATA) hsdRendonuclease R
Reads supporting (aligned to +/- strand):  ref base G (39/24);  new base A (3/2);  total (42/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

CGCACAGGCGATGGCATAAGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCTTAGCTTTCTG  >  W3110S.gb/4591375‑4591514
                                                                      |                                                                     
cgcACAGGCGATGGCATAAGTGAAGTCGTTGCCGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTg                                                                       >  1:3416692/1‑71 (MQ=255)
cgcACAGGCGATGGCATAAGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTg                                                                       >  1:2367340/1‑71 (MQ=255)
      ggCGATGGCATAAGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGttatt                                                                  >  1:1181325/1‑70 (MQ=255)
       gCGATGGCATAAGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTATTATTaa                                                                >  1:2117528/1‑71 (MQ=255)
           tGGCATAAGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCa                                                            >  1:1033792/1‑71 (MQ=255)
             gCATAAGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCAt                                                           <  1:4223695/70‑1 (MQ=255)
             gCATAAGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCAt                                                           <  1:2079126/70‑1 (MQ=255)
              cATAAGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTg                                                         <  1:599330/71‑1 (MQ=255)
                 aaGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCtg                                                      >  1:4051081/1‑71 (MQ=255)
                  aGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCtgt                                                     >  1:2557806/1‑71 (MQ=255)
                   gTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCtgtg                                                    <  1:2074683/71‑1 (MQ=255)
                    tGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGc                                                   >  1:4190382/1‑71 (MQ=255)
                     gAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCg                                                  >  1:3365265/1‑71 (MQ=255)
                     gAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTATTATTAAt                                                               >  1:729904/1‑58 (MQ=255)
                       aGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCggg                                                >  1:1493839/1‑71 (MQ=255)
                        gTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATcc                                                             <  1:2743786/57‑1 (MQ=255)
                         tCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTg                                                                       <  1:2063801/46‑1 (MQ=255)
                          cGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGAGGGCCt                                             >  1:439703/1‑71 (MQ=255)
                            ttGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGttat                                                                   <  1:3759990/47‑1 (MQ=255)
                              gACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATc                                                              >  1:3162739/1‑50 (MQ=255)
                              gACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCggg                                                >  1:1359570/1‑64 (MQ=255)
                                 gCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTg                                            <  1:1738473/65‑1 (MQ=255)
                                 gCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCaaa                                      <  1:369262/71‑1 (MQ=255)
                                   ccTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAata                                    >  1:2278040/1‑71 (MQ=255)
                                    cTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATc                                                              <  1:2818940/44‑1 (MQ=255)
                                     ttCAGGAATTCAAAATTGGATTTATTCATCATTGtt                                                                     <  1:1320917/36‑1 (MQ=255)
                                       cAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCTAAATAtt                                  <  1:1950515/69‑1 (MQ=255)
                                       cAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATAttt                                 <  1:1890376/70‑1 (MQ=255)
                                       cAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATAtt                                  <  1:3175879/69‑1 (MQ=255)
                                       aaGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATAttt                                 <  1:789710/69‑1 (MQ=255)
                                        aGGAATTCAAAATTGGATTTATTCATCATTGttatt                                                                  <  1:2258156/36‑1 (MQ=255)
                                        aGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATAttt                                 >  1:205015/1‑69 (MQ=255)
                                           aaTTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGc                            >  1:2542442/1‑71 (MQ=255)
                                            aTTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGcc                           <  1:4522944/71‑1 (MQ=255)
                                            aTTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGcc                           >  1:1394519/1‑71 (MQ=255)
                                             ttCAAAATTGGATTTATTCATCATTGTTATTAATc                                                              >  1:2127060/1‑35 (MQ=255)
                                             ttCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGccc                          <  1:1542422/71‑1 (MQ=255)
                                               cAATATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCa                         >  1:1060066/1‑70 (MQ=255)
                                               cAAAATTGGATTTATTCATCATTGTTATTAATCCAt                                                           >  1:3259454/1‑36 (MQ=255)
                                               cAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCtg                                                      >  1:905878/1‑41 (MQ=255)
                                               cAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCt                                                       >  1:2702120/1‑40 (MQ=255)
                                               cAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCa                         >  1:2940650/1‑70 (MQ=255)
                                                aaaaTTGGATTTATTCATCATTGTTATTAATCCAt                                                           >  1:2808424/1‑35 (MQ=255)
                                                aaaaTTGGATTTATTCATCATTGTTATTAATCCAt                                                           >  1:1195586/1‑35 (MQ=255)
                                                  aaTTGGATTTATTCATCATTGTTATTAATCCATTGCtgt                                                     >  1:1942410/1‑39 (MQ=255)
                                                  aaTTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAatat                                   >  1:3181578/1‑57 (MQ=255)
                                                  aaTTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATaa                      >  1:3653255/1‑70 (MQ=255)
                                                  aaTTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATaa                      >  1:608838/1‑70 (MQ=255)
                                                   aTTGGATTTATTCATCATTGTTATTAATCCATTGCtgt                                                     <  1:1132399/38‑1 (MQ=255)
                                                   aTTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTcc                                         <  1:318328/50‑1 (MQ=255)
                                                   aTTGGATTTATTCATCATTATTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCAt                        >  1:2403447/1‑67 (MQ=255)
                                                      ggATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAAcatct                 >  1:312619/1‑71 (MQ=255)
                                                        aTTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAatat                                   <  1:4291982/51‑1 (MQ=255)
                                                        aTTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAAcatctca               >  1:708028/1‑71 (MQ=255)
                                                          ttATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAAcatctcatc             >  1:2663476/1‑71 (MQ=255)
                                                          ttATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAAcatctcatc             >  1:3811292/1‑71 (MQ=255)
                                                          ttATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAAcatctcatc             >  1:3896909/1‑71 (MQ=255)
                                                          ttATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAAcatctcatc             >  1:3902133/1‑71 (MQ=255)
                                                             ttCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCtt           <  1:4489153/70‑1 (MQ=255)
                                                             ttCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCTTa          <  1:1040373/71‑1 (MQ=255)
                                                             ttCATCATTATTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCtt           <  1:2600220/70‑1 (MQ=255)
                                                              tcatcaTTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCTTa          >  1:564067/1‑70 (MQ=255)
                                                                atcatTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATa                       <  1:1322514/55‑1 (MQ=255)
                                                                atcatTATTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCTTAGCt       <  1:128514/71‑1 (MQ=255)
                                                                  catTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAat                                     >  1:1853201/1‑39 (MQ=255)
                                                                  catTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAgg                             >  1:2351140/1‑47 (MQ=255)
                                                                  catTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCTTAGCttt     >  1:2947009/1‑71 (MQ=255)
                                                                  catTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCTTAGCtt      >  1:42059/1‑70 (MQ=255)
                                                                  catTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCTTAGCtt      >  1:359961/1‑70 (MQ=255)
                                                                    ttGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCTTAGCt       <  1:4021132/67‑1 (MQ=255)
                                                                     tGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCTTAGCTTTCTg  >  1:4136171/1‑71 (MQ=255)
                                                                      |                                                                     
CGCACAGGCGATGGCATAAGTGAAGTCGTTGACGCCCTTCAGGAATTCAAAATTGGATTTATTCATCATTGTTATTAATCCATTGCTGTGCGGGCCTGTCCAAATATTTAAGGCCCATAACATCTCATCTTAGCTTTCTG  >  W3110S.gb/4591375‑4591514

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