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 2,377,802 A→T 31.7% Y196N (TAC→AAC)  ubiB ← 2‑octaprenylphenol hydroxylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,377,8020AT31.7% 86.9 / 53.5 63Y196N (TAC→AAC) ubiB2‑octaprenylphenol hydroxylase
Reads supporting (aligned to +/- strand):  ref base A (28/15);  new base T (14/6);  total (42/21)
Fisher's exact test for biased strand distribution p-value = 7.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

TGCGCCGAAGCTGAATGGCGTTGGCAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCGGCACCCAGCGAGCCA  >  minE/2377733‑2377870
                                                                     |                                                                    
tGCGCCGAAGCTGAATGGCGTTGGCAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTAc                                                                     >  1:1636824/1‑71 (MQ=255)
tGCGCCGAAGCTGAATGGCGTTGGCAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTAc                                                                     >  1:3014042/1‑71 (MQ=255)
      gAAGCTGAATGGCGTTGGCAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTTCTCgcgc                                                               <  1:1699272/71‑1 (MQ=255)
            gAATGGCGTTGGCAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACt                                                                    >  1:3772917/1‑60 (MQ=255)
            gAATGGCGTTGGCAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACt                                                         >  1:1901337/1‑71 (MQ=255)
                      ggCAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTCGGTTGGgc                                               >  1:366813/1‑71 (MQ=255)
                        cAGTTTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTCGGTTGGgcgc                                             <  1:2501737/71‑1 (MQ=255)
                        cAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTcgc                                                                 <  1:3724608/51‑1 (MQ=255)
                        cAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTcgc                                                                 <  1:3547282/51‑1 (MQ=255)
                        cAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTCGGTTGGgcg                                              >  1:3952141/1‑70 (MQ=255)
                        cAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTCGGTTGGgcg                                              >  1:72576/1‑70 (MQ=255)
                         aGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTCGGTTGGTCGCa                                            <  1:2847909/71‑1 (MQ=255)
                           aTTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGa                                          >  1:1647516/1‑71 (MQ=255)
                            ttCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGAc                                         >  1:3018824/1‑71 (MQ=255)
                                cGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCAGACGGCg                                     <  1:2370752/71‑1 (MQ=255)
                                 gcagcaAATTCAGTTCATCAATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGgcgaa                                            >  1:1146641/1‑61 (MQ=255)
                                 gcagcaAATTCAGTTCATCAATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCa                                            >  1:480996/1‑63 (MQ=255)
                                 gcagcaAATTCAGTTCATCAATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCa                                            >  1:191021/1‑63 (MQ=255)
                                 gcagcaAATTCAGTTCATCAATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCa                                            >  1:4255863/1‑63 (MQ=255)
                                 gcagcaAATTCAGTTCATCAATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCa                                            >  1:1845807/1‑63 (MQ=255)
                                 gcagcaAATTCAGTTCATCAATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCa                                            >  1:1887941/1‑63 (MQ=255)
                                 gcagcaAATTCAGTTCATCAATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCa                                            >  1:1609551/1‑63 (MQ=255)
                                         ttCAGTTCATCAATCAATGTCTTTTCGTACTCgcgc                                                               <  1:2036166/36‑1 (MQ=255)
                                         ttCAGTTCATCAATCAATGTCTTTTCGTACTCgcgc                                                               <  1:1279196/36‑1 (MQ=255)
                                         ttCAGTTCATCAATCAATGTCTTTTCGTACTCgcgc                                                               <  1:3197574/36‑1 (MQ=255)
                                         ttCAGTTCATCAATCAATGTCTTTTCGTACTCGCTCACCACTTc                                                       <  1:2057383/44‑1 (MQ=255)
                                         ttCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTc                                                       <  1:3852556/44‑1 (MQ=255)
                                         ttCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTc                                                       <  1:360779/44‑1 (MQ=255)
                                         ttCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTc                                                       <  1:744470/44‑1 (MQ=255)
                                           cAGTTCATCAATCAATGTCTTTTCGTACTCGCGcac                                                             >  1:3342758/1‑36 (MQ=255)
                                           cAGTTCATCAATCAATGTCTTTTCGTACTCGCGcac                                                             >  1:287081/1‑36 (MQ=255)
                                                catcaATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCaaa                     >  1:3260319/1‑71 (MQ=255)
                                                catcaATCAATGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCaaa                     >  1:1963845/1‑71 (MQ=255)
                                                catcaATCAATGTCTTTTCGTACTCGCGCACCACTTCGGt                                                    >  1:87272/1‑40 (MQ=255)
                                                catcaATCAATGTCTTTTCGTACTCGCGCACCACTTCGGt                                                    >  1:1154375/1‑40 (MQ=255)
                                                catcaATCAATGTCTTTTCGTACTCGCGCACCACTTCGGt                                                    >  1:1492160/1‑40 (MQ=255)
                                                catcaATCAATGTCTTTTCGTACTCGCGCACCACTTCGGt                                                    >  1:2978134/1‑40 (MQ=255)
                                                catcaATCAATGTCTTTTCGTACTCGCGCACCACTTCGGt                                                    >  1:1750698/1‑40 (MQ=255)
                                                catcaATCAATGTCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCaaa                     >  1:293797/1‑71 (MQ=255)
                                                  tcaatcaaTGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGACGGCGAc                                   <  1:285951/55‑1 (MQ=255)
                                                  tcaatcaaTGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGACGGCGAc                                   <  1:1088162/55‑1 (MQ=255)
                                                  tcaatcaaTGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAAcg                   <  1:3676359/71‑1 (MQ=255)
                                                  tcaatcaaTGTCTTTTCGTACTCGCGCACCACTTCGGTTgg                                                 >  1:2123501/1‑41 (MQ=255)
                                                  tcaatcaaTGTCTTTTCGTACTCGCGCACCACTTCGGTTgg                                                 >  1:3886271/1‑41 (MQ=255)
                                                  tcaatcaaTGTCTTTTCGTACTCGCGCACCACTTCGGTTgg                                                 >  1:1359778/1‑41 (MQ=255)
                                                  tcaatcaaTGTCTTTTCGTACTCGCGCACCACTTCGGTTgg                                                 >  1:2571278/1‑41 (MQ=255)
                                                    aatcaatGTCTTTTCGTACTCGCGCACCACTTCGGTTAGGCGCAGACGGCGACCATCCGGCAGCAAAcgc                  <  1:1052298/70‑1 (MQ=255)
                                                        aatGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCGGCa              <  1:2293387/70‑1 (MQ=255)
                                                        aatGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCGGCAc             >  1:1811956/1‑71 (MQ=255)
                                                        aatGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCGGCAc             >  1:854998/1‑71 (MQ=255)
                                                        aatGTCTTTTCGTTCTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCGGCAc             >  1:794761/1‑71 (MQ=255)
                                                        aatGTCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCa                                            <  1:1203776/40‑1 (MQ=255)
                                                        aatGTCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCAGAc                                         >  1:853775/1‑43 (MQ=255)
                                                        aatGTCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCAGAc                                         >  1:2745484/1‑43 (MQ=255)
                                                        aatGTCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCAGAc                                         >  1:3110356/1‑43 (MQ=255)
                                                            tCTTTTCGTACTCGCGCACCACTTCGGTTGGgcgc                                             >  1:2781704/1‑35 (MQ=255)
                                                            tCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCa                                            >  1:3306160/1‑36 (MQ=255)
                                                            tCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCa                                            >  1:2222571/1‑36 (MQ=255)
                                                            tCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCGGCACCCAg         >  1:1112765/1‑71 (MQ=255)
                                                            tCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCGGCACCCAg         >  1:1078125/1‑71 (MQ=255)
                                                            tCTTTTAGTACTCGCGCAACACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCGGCACCCAg         >  1:1504921/1‑71 (MQ=255)
                                                                ttCGTTCTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCGGCACCCAGCGa      <  1:3554462/70‑1 (MQ=255)
                                                                   gTACTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCTGCACCCAGCGAGCCa  <  1:286242/71‑1 (MQ=255)
                                                                     |                                                                    
TGCGCCGAAGCTGAATGGCGTTGGCAGATTCCCGCAGCAAATTCAGTTCATCAATCAATGTCTTTTCGTACTCGCGCACCACTTCGGTTGGGCGCAGACGGCGACCATCCGGCAGCAAACGCGGCACCCAGCGAGCCA  >  minE/2377733‑2377870

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