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
A6 F1 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,474,821	T→G	26.7%	intergenic (+119/‑115)	nrdA → / → nrdB	ribonucleoside diphosphate reductase 1, alpha subunit/ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,474,821	0	T	G	26.7%	58.6 / 19.6	30	intergenic (+119/‑115)	nrdA/nrdB	ribonucleoside diphosphate reductase 1, alpha subunit/ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like
Reads supporting (aligned to +/- strand): ref base T (16/6); new base G (6/2); total (22/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.32e-02

GTTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCG  >  minE/1474752‑1474889

gTTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTa                                                                      <  1:1571196/71‑1 (MQ=255)

gTTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTa                                                                      <  1:3915434/71‑1 (MQ=255)

gTTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTa                                                                      <  1:2315959/71‑1 (MQ=255)

                    gcgcCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATcc                                                                   >  1:2005419/1‑54 (MQ=255)

                    gcgcCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑tt                                                 <  1:3803575/71‑1 (MQ=255)

                        cAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTg                                               >  1:5391049/1‑69 (MQ=255)

                               gCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGa                                      <  1:5172349/71‑1 (MQ=255)

                                   cAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGAt                                     >  1:4350047/1‑68 (MQ=255)

                                    aGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTAt                                                                     >  1:4150126/1‑36 (MQ=255)

                                    aGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAc                                                            >  1:106070/1‑45 (MQ=255)

                                    aGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGa                                 >  1:1587807/1‑71 (MQ=255)

                                          cGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACgcgc                            >  1:2051645/1‑70 (MQ=255)

                                            tgTGCTGGACGTAGCGTAAACGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGAcgcgg                            >  1:1857138/2‑68 (MQ=2)

                                            tgTGCTGGACGTAGCGTAAACGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGAcgcgg                            >  1:4615802/2‑68 (MQ=2)

                                             gTGCTGGACGTAGCGTAAACGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGAcgcggt                           <  1:2532356/69‑3 (MQ=2)

                                                   gATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCa                  >  1:77001/1‑71 (MQ=255)

                                                   gATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCa                  >  1:5542865/1‑71 (MQ=255)

                                                    aTGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCAt                 >  1:661098/1‑71 (MQ=255)

                                                       cAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAg              >  1:2206749/1‑71 (MQ=255)

                                                        aGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑tt                                                 >  1:5494721/1‑35 (MQ=255)

                                                        aGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑tt                                                 >  1:922637/1‑35 (MQ=255)

                                                        aGCGTAAACGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCAt                 >  1:5051680/1‑68 (MQ=2)

                                                            taaaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGACGCGGTAGCGTc                     >  1:3925360/3‑60 (MQ=2)

                                                            taaaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCATCAGGcat          <  1:5142320/69‑2 (MQ=2)

                                                             gAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAg        >  1:5173600/1‑71 (MQ=255)

                                                              aaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGa                                 >  1:431275/1‑46 (MQ=9)

                                                              aaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGAcgcg                             >  1:4923270/1‑50 (MQ=9)

                                                                 gCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATg    >  1:1205345/1‑71 (MQ=255)

                                                                  ccTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgc   >  1:5169314/1‑71 (MQ=255)

                                                                   cTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgcg  <  1:2114059/71‑1 (MQ=255)

                                                                     tATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCg                       <  1:2806915/48‑1 (MQ=255)

GTTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCG  >  minE/1474752‑1474889

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