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	1,493,345	G→A	60.8%	C28C (TGC→TGT)	nuoH ←	NADH:ubiquinone oxidoreductase, membrane subunit H

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,493,345	0	G	A	60.8%	25.9 / 42.1	65	C28C (TGC→TGT)	nuoH	NADH:ubiquinone oxidoreductase, membrane subunit H
Reads supporting (aligned to +/- strand): ref base G (19/6); new base A (19/20); total (39/26)
Fisher's exact test for biased strand distribution p-value = 3.87e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01

TAGGTCCGTAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATCACCACCGCTTTGAGGATGGTCAGCAGGATCTCAATC  >  minE/1493281‑1493405

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:439410/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:1850053/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:3250976/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:3332184/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:1557010/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:2415172/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:3404406/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:3209761/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:2159548/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:371625/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:405278/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:1356532/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:1345456/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:2180312/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:622235/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:1260344/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:3207521/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:1188458/69‑1 (MQ=255)

tAGGTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:623959/69‑1 (MQ=255)

  ggTCCATAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAgg                                                          <  1:1034254/67‑1 (MQ=255)

      cGTAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACa                                                     >  1:3088021/1‑68 (MQ=255)

      cGTAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACa                                                     >  1:3021693/1‑68 (MQ=255)

      cGTAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACa                                                     >  1:585965/1‑68 (MQ=255)

                     aCAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATc                                      <  1:2752715/68‑1 (MQ=255)

                       aGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCTCAGGTGACTACCACCAGCAGGATcacc                                   >  1:1408321/1‑69 (MQ=255)

                       aGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGATcac                                    >  1:123335/1‑68 (MQ=255)

                        gACCGAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATcacc                                   >  1:192237/1‑68 (MQ=255)

                        gACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATcacca                                  >  1:2619109/1‑69 (MQ=255)

                        gACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATcacca                                  >  1:2274474/1‑69 (MQ=255)

                        gACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATcacca                                  >  1:3220392/1‑69 (MQ=255)

                        gACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATcacca                                  >  1:3393010/1‑69 (MQ=255)

                        gACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATcacca                                  >  1:1419607/1‑69 (MQ=255)

                        gACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATcacca                                  >  1:946171/1‑69 (MQ=255)

                        gACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATcacc                                   >  1:2547687/1‑68 (MQ=255)

                        gACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATcacc                                   >  1:137688/1‑68 (MQ=255)

                                  gCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATCACCACCGCTTTGAg                        <  1:2574812/69‑1 (MQ=255)

                                  gCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATCACCACCGCTTTGAg                        <  1:181164/69‑1 (MQ=255)

                                  gCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATCACCACCGCTTTGAg                        <  1:2125007/69‑1 (MQ=255)

                                  gCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATCACCACCGCTTTGAg                        <  1:819967/69‑1 (MQ=255)

                                  gCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATCACCACCGCTTTGAg                        <  1:820736/69‑1 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACcagc                                            >  1:797119/1‑47 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACcagc                                            >  1:795623/1‑47 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACcagc                                            >  1:2781924/1‑47 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACcagc                                            >  1:1549715/1‑47 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACcag                                             >  1:1724979/1‑46 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGa                                                       >  1:2079335/1‑36 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGCCTACCACCCGCAGGAt                                       >  1:1169995/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGa                                        >  1:476441/1‑51 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:1266717/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:13697/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:418905/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:1376537/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:1089855/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:3436203/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:1467162/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:2182255/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:2240881/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:3054563/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:2441772/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:289253/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:2852964/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:2487604/1‑52 (MQ=255)

                                    gACGTTCGCCAAAGCTCATGAATGCCCCACAGGTGACTACCACCAGCAGGAt                                       >  1:2641380/1‑52 (MQ=255)

                                                        aaTGCCCCGCAGGTGACAACCACCAGCAGGATCACCACCGCTTTGAGGATGGTCAGCAGGATCTCAAt   >  1:3303772/1‑68 (MQ=255)

                                                        aaTGCCCCGCAGGTGACAACCACCAGCAGGATCACCACCGCTTTGAGGATGGTCAGCAGGATCTCAATc  >  1:1265680/1‑69 (MQ=255)

TAGGTCCGTAACGGTTCTGGAACAGACCCAGCAGGCGACGTTCGCCAAAGCTCATGAATGCCCCGCAGGTGACAACCACCAGCAGGATCACCACCGCTTTGAGGATGGTCAGCAGGATCTCAATC  >  minE/1493281‑1493405

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