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	384,705	A→G	37.3%	intergenic (+95/‑86)	ybdB → / → cstA	conserved hypothetical protein/carbon starvation protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	384,705	0	A	G	37.3%	90.9 / 100.1	154	intergenic (+95/‑86)	ybdB/cstA	conserved hypothetical protein/carbon starvation protein
Reads supporting (aligned to +/- strand): ref base A (34/62); new base G (16/41); total (51/103)
Fisher's exact test for biased strand distribution p-value = 3.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 154 total aligned reads displayed.

AACTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATCTCTA  >  minE/384641‑384766

aaCTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATg                                                           <  1:957630/69‑1 (MQ=255)

aaCTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATg                                                           <  1:8864/69‑1 (MQ=255)

aaCTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATg                                                           <  1:515915/69‑1 (MQ=255)

aaCTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATg                                                           <  1:1267294/69‑1 (MQ=255)

aaCTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATg                                                           <  1:389139/69‑1 (MQ=255)

aaCTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATg                                                           <  1:2886075/69‑1 (MQ=255)

aaCTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATg                                                           <  1:2553824/69‑1 (MQ=255)

aaCTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATg                                                           <  1:1357464/69‑1 (MQ=255)

aaCTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATg                                                           <  1:1723058/69‑1 (MQ=255)

            ggAGTGATCGAGTTAAGATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgttg                                               <  1:1935115/69‑1 (MQ=255)

            ggAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgttg                                               <  1:105245/69‑1 (MQ=255)

            ggAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgttg                                               <  1:205821/69‑1 (MQ=255)

            ggAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgttg                                               <  1:1940181/69‑1 (MQ=255)

            ggAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgttg                                               <  1:1494714/69‑1 (MQ=255)

            ggAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgttg                                               <  1:1128011/69‑1 (MQ=255)

             gAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgttg                                               <  1:1621469/68‑1 (MQ=255)

             gAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgttg                                               <  1:1971818/68‑1 (MQ=255)

               gTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCtg                                                    >  1:2139927/1‑61 (MQ=255)

                  aTCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAATTCCGATTTACATGGTTGCTGTGTTGTTAAAt                                         >  1:1563769/1‑69 (MQ=255)

                  aTCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAATTCCGATTTACATGGTTGCTGTGTTGTTAAAt                                         >  1:58715/1‑69 (MQ=255)

                  aTCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAAt                                         <  1:1569064/69‑1 (MQ=255)

                  aTCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAAt                                         <  1:2998112/69‑1 (MQ=255)

                  aTCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAAt                                         <  1:815828/69‑1 (MQ=255)

                  aTCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAAt                                         <  1:2215923/69‑1 (MQ=255)

                  aTCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAAt                                         >  1:1276325/1‑69 (MQ=255)

                   tCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAAt                                         <  1:2140514/68‑1 (MQ=255)

                    cGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTg                                       >  1:2950710/1‑69 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTTCATGGTTGCTGtgtt                                                >  1:727254/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:189767/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:1463040/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:276992/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:2641083/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:2603469/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:3059070/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:2363812/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:912183/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:3179265/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:1399538/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:2100664/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:1659196/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTGCATGGTTGCTGtgtt                                                >  1:3194211/1‑54 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACaaa                                 <  1:3317326/69‑1 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACaaa                                 <  1:28765/69‑1 (MQ=255)

                          aaCATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACaaa                                 <  1:2555289/69‑1 (MQ=255)

                             aTTGTTAAGTTAAATATTGGGTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACaaa                                 <  1:2851704/66‑1 (MQ=255)

                               tGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAAt                                         <  1:777404/56‑1 (MQ=255)

                               tGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGa                               <  1:1442570/66‑1 (MQ=255)

                               tGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGa                               <  1:3399181/66‑1 (MQ=255)

                                gttaagttaaATATTGGGTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAAt                                         <  1:2709067/55‑1 (MQ=255)

                                            atTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTTTTAAAt                                         <  1:1575760/43‑1 (MQ=255)

                                            atTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACaaaa               >  1:1425716/1‑69 (MQ=255)

                                             ttGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACaaaa               >  1:2090009/1‑68 (MQ=255)

                                             ttGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACaaaa               >  1:3324997/1‑68 (MQ=255)

                                             ttGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACaaaa               >  1:791100/1‑68 (MQ=255)

                                             ttGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACaaaa               >  1:1297049/1‑68 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:318936/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:2999426/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:3295726/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:3241923/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:377389/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:620278/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:92154/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:1612251/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:1623632/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:1648827/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:1809207/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:866033/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:2067834/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:2220471/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:2338953/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:1334105/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:2587856/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:730927/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:2688293/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTGCATGGTTGCTGTGTTGTTAAATTg                                       <  1:2884588/39‑1 (MQ=255)

                                                  ttCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGt            >  1:522588/1‑66 (MQ=255)

                                                  ttCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGt            >  1:77739/1‑66 (MQ=255)

                                                  ttCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGt            >  1:1110284/1‑66 (MQ=255)

                                                  ttCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGt            >  1:569654/1‑66 (MQ=255)

                                                  ttCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGt            >  1:2797733/1‑66 (MQ=255)

                                                  ttCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGt            >  1:2936371/1‑66 (MQ=255)

                                                  ttCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGt            >  1:2788824/1‑66 (MQ=255)

                                                  ttCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGt            >  1:1389700/1‑66 (MQ=255)

                                                  ttCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGt            >  1:3423557/1‑66 (MQ=255)

                                                  ttCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTaa          <  1:1565662/68‑1 (MQ=255)

                                                   tCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACaaa                                 <  1:3096061/44‑1 (MQ=255)

                                                   tCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACaaa                                 <  1:2276784/44‑1 (MQ=255)

                                                   tCAACTCCGATATACATGGTTGCTGTGTTGTTAAATTGTACaaa                                 <  1:668799/44‑1 (MQ=255)

                                                       cTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACAtctc    <  1:1029532/69‑1 (MQ=255)

                                                        tCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATctct   <  1:266015/69‑1 (MQ=255)

                                                        tCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATctct   <  1:1613741/69‑1 (MQ=255)

                                                        tCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATctct   <  1:2004143/69‑1 (MQ=255)

                                                        tCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATctct   <  1:2406542/69‑1 (MQ=255)

                                                        tCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATctct   <  1:2569573/69‑1 (MQ=255)

                                                        tCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATctct   <  1:269117/69‑1 (MQ=255)

                                                        tCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATctct   <  1:57404/69‑1 (MQ=255)

                                                        tCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATctct   <  1:3238090/69‑1 (MQ=255)

                                                         ccGATTTACATGGTTGCTGTGTTGTTAAATTGTACaaa                                 >  1:2336818/1‑38 (MQ=255)

                                                         ccGATTTACATGGTTGCTGTGTTGTTAAATTGTACaaa                                 >  1:305547/1‑38 (MQ=255)

                                                         ccGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATCTCTa  >  1:2891924/1‑69 (MQ=255)

AACTCGGTTAACGGAGTGATCGAGTTAACATTGTTAAGTTAAATATTGGTTTCAACTCCGATTTACATGGTTGCTGTGTTGTTAAATTGTACAAAGATGTTATAGAAACAAAATGTAACATCTCTA  >  minE/384641‑384766

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