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 2,676,550 A→T 61.4% Q100L (CAG→CTG)  bioH → carboxylesterase of pimeloyl‑CoA synthesis

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,676,5500AT61.4% 45.8 / 62.4 70Q100L (CAG→CTG) bioHcarboxylesterase of pimeloyl‑CoA synthesis
Reads supporting (aligned to +/- strand):  ref base A (12/15);  new base T (22/21);  total (34/36)
Fisher's exact test for biased strand distribution p-value = 6.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGTTAGGCTGGAGTCTGGGCGGGCTGGTGGCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGTGACGAGTGGCCGGGGAT  >  minE/2676483‑2676610
                                                                   |                                                            
tGGTTAGGCTGGAGTCTGGGCGGGCTGGTGGCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAg                                                             >  1:2510267/1‑69 (MQ=255)
tGGTTAGGCTGGAGTCTGGGCGGGCTGGTGGCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAg                                                             >  1:814544/1‑69 (MQ=255)
   ttAGGCTGGAGTCTGGGCGGGCTGGTGGCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGgc                                                           <  1:1569367/68‑1 (MQ=255)
           gAGTCTGGGCGGGCTGGTGGCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCAc                                                  >  1:1406126/1‑69 (MQ=255)
           gAGTCTGGGCGGGCTGGTGGCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCAc                                                  >  1:2399309/1‑69 (MQ=255)
           gAGTCTGGGCGGGCTGGTGGCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCAc                                                  >  1:593573/1‑69 (MQ=255)
           gAGTCTGGGCGGGCTGGTGGCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCAc                                                  >  1:2817993/1‑69 (MQ=255)
           gAGTCTGGGCGGGCTGGTGGCAAGCCAGATTGAGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCAc                                                  >  1:2633542/1‑69 (MQ=255)
                         tggtggCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCAc                                    <  1:2138899/69‑1 (MQ=255)
                         tggtggCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCAc                                    <  1:2311266/69‑1 (MQ=255)
                         tggtggCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCAc                                    <  1:2591842/69‑1 (MQ=255)
                         tggtggCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCAc                                    <  1:721502/69‑1 (MQ=255)
                         tggtggCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCAc                                    <  1:525181/69‑1 (MQ=255)
                         tggtggCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCAc                                    <  1:1424490/69‑1 (MQ=255)
                                 aGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGtttt                            <  1:2829419/69‑1 (MQ=255)
                                 aGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGtttt                            <  1:1494738/69‑1 (MQ=255)
                                 aGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGtttt                            <  1:1864559/69‑1 (MQ=255)
                                 aGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGtttt                            <  1:1878156/69‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGttt                             >  1:3300357/1‑60 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGttt                             >  1:2321382/1‑60 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGttt                             >  1:56696/1‑60 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGttt                             <  1:2221760/60‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGttt                             <  1:1004459/60‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGttt                             <  1:2002/60‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGttt                             <  1:1687856/60‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:2771670/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:3331665/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:1488399/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:3332908/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:3355066/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:3179639/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:2871556/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:3362268/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:2721257/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:2646941/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:1689837/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:3435306/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:1732028/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:2369170/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:1455439/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:55679/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:816963/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:2076787/57‑1 (MQ=255)
                                         tGCGTTAACCCATCCAGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGttt                             >  1:1526903/1‑60 (MQ=255)
                                         tGCGTTAACCCAACCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:3074085/57‑1 (MQ=255)
                                               aaCCCATCGCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTg                                <  1:468884/51‑1 (MQ=255)
                                                    aTCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCCCCGTGTTTTa                           >  1:825041/1‑51 (MQ=255)
                                                    aTCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCgcg                  >  1:3000719/1‑58 (MQ=255)
                                                    aTCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGc         >  1:2062936/1‑69 (MQ=255)
                                                    aTCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGc         >  1:900649/1‑69 (MQ=255)
                                                    aTCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGc         >  1:630226/1‑69 (MQ=255)
                                                    aTCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGc         >  1:1942604/1‑69 (MQ=255)
                                                    aTCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGc         >  1:2324553/1‑69 (MQ=255)
                                                    aTCCCGAGCGGGTTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGc         >  1:1947645/1‑69 (MQ=255)
                                                          aGCGGGTGCTGGCGCTGGCCACCGTGGCGTCGTCACCTTg                                <  1:650745/40‑1 (MQ=25)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTTGTGCTCGCGACGAGTGGCCGGGGAt  >  1:817662/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:896495/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:94824/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:3304752/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:3285890/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:3270743/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:2971457/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:2814910/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:1948181/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:1692275/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:1671105/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:1654305/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:1467041/4‑68 (MQ=255)
                                                            cgggtTCTGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGCGACGAGTGGCCGGGGAt  >  1:1250971/4‑68 (MQ=255)
                                                            cGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGTGACGAGTGGCCGGGGa   >  1:779284/1‑67 (MQ=255)
                                                                   |                                                            
TGGTTAGGCTGGAGTCTGGGCGGGCTGGTGGCAAGCCAGATTGCGTTAACCCATCCCGAGCGTGTTCAGGCGCTGGTCACCGTGGCGTCGTCACCTTGTTTTAGTGCTCGTGACGAGTGGCCGGGGAT  >  minE/2676483‑2676610

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