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	2,009,730	G→T	61.2%	pseudogene (297/411 nt)	yghX ←	ECK2993:JW5926:b2999; predicted hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,009,730	0	G	T	61.2%	9.5 / 26.1	31	pseudogene (297/411 nt)	yghX	ECK2993:JW5926:b2999; predicted hydrolase
Reads supporting (aligned to +/- strand): ref base G (6/6); new base T (13/6); total (19/12)
Fisher's exact test for biased strand distribution p-value = 4.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01

GATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATAGATATACGCCTCATAAACCTTATTATTGGCTTTCAACGCCGCCTCGTA  >  minE/2009663‑2009777

gATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                <  1:1004800/69‑1 (MQ=255)

gATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                <  1:805544/69‑1 (MQ=255)

gATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                <  1:1057032/69‑1 (MQ=255)

gATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                <  1:2112248/69‑1 (MQ=255)

gATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                <  1:3127522/69‑1 (MQ=255)

gATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                <  1:310641/69‑1 (MQ=255)

gATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                <  1:3038228/69‑1 (MQ=255)

gATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                <  1:2804455/69‑1 (MQ=255)

gATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                <  1:2773690/69‑1 (MQ=255)

gATCGGCGGCAGAATTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                <  1:2617725/69‑1 (MQ=255)

 aTCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                >  1:3249171/1‑68 (MQ=255)

 aTCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                >  1:2255096/1‑68 (MQ=255)

 aTCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgataga                                                >  1:1964586/1‑68 (MQ=255)

  tCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgatagata                                              <  1:2223638/69‑1 (MQ=255)

  tCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgatagata                                              <  1:1033079/69‑1 (MQ=255)

  tCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgatagata                                              <  1:2380196/69‑1 (MQ=255)

  tCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgatagata                                              <  1:2586206/69‑1 (MQ=255)

  tCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgatagata                                              <  1:2946119/69‑1 (MQ=255)

  tCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgatagata                                              <  1:3426786/69‑1 (MQ=255)

  tCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgatagata                                              <  1:355892/69‑1 (MQ=255)

  tCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgatagata                                              <  1:1075069/69‑1 (MQ=255)

  tCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGgatagata                                              <  1:1370830/69‑1 (MQ=255)

            aTTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCAt                                    <  1:1035614/69‑1 (MQ=255)

              ttGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATag                                  <  1:3159541/69‑2 (MQ=255)

              ttGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATag                                  <  1:1160618/69‑2 (MQ=255)

              ttGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATag                                  <  1:1560260/69‑2 (MQ=255)

              ttGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATag                                  <  1:3084876/69‑2 (MQ=255)

               tGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATag                                  <  1:2155894/68‑2 (MQ=255)

                 tCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATAGATATACGCCTCATAAAc                                <  1:2088648/68‑1 (MQ=255)

                 tCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATAGATATACGCCTCATAAAc                                <  1:610425/68‑1 (MQ=255)

                 tCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATAGATATACGCCTCATAAAc                                <  1:599990/68‑1 (MQ=255)

                   aTAACGGGGCGTGGAATCATTATGTAATCCGTGATTAACCCCCGgatagata                                              <  1:1152709/52‑1 (MQ=255)

                      aCGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATAGATATACGCCTCATAAACCttatt                          <  1:516251/69‑1 (MQ=255)

                      aCGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATAGATATACGCCTCATAAACCttat                           <  1:371647/68‑1 (MQ=255)

                        ggggCGTGGAGTCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:759964/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:1096500/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:2082063/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:795296/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:674882/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:2389990/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:2484694/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:454117/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:322945/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:314336/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:3133064/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:192212/1‑69 (MQ=255)

                        ggggCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATATATATACGCCTCATAGACCTtattat                        >  1:1544170/1‑69 (MQ=255)

                           gCGTGGAATCATTATGGAATCCGTGATTAACCCCCGTATAGatat                                             >  1:698216/1‑45 (MQ=255)

                           gCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATAGATATACGCCTCATAAACCTTATTATTgc                     >  1:2046916/1‑68 (MQ=255)

                                gAATCATTATGGAATCCGTGATTAACCCCCGGATAGATATACGCCTCATAAACCTTATTATTGGCTTTc                <  1:2079000/69‑1 (MQ=255)

                                                cGTGATTAACCCCCGGATAGATATACGCCTCATAAACCTTATTATTGGCTTTCAACGCCGCCTCGTa  >  1:297925/1‑67 (MQ=255)

                                                cGTGATTAACCCCCGGATAGATATACGCCTCATAAACCTTATTATTGGCTTTCAACGCCGCCTCGTa  >  1:2709200/1‑67 (MQ=255)

                                                cGTGATTAACCCCCGGATAGATATACGCCTCATAAACCTTATTATTGGCTTTCAACGCCGCCTCGTa  >  1:1388606/1‑67 (MQ=255)

                                                cGTGATTAACCCCCGGATAGATATACGCCTCATAAACCTTATTATTGGCTTTAAACGCCGCCTCGTa  >  1:3419452/1‑67 (MQ=255)

GATCGGCGGCAGATTTGTCATAACGGGGCGTGGAATCATTATGGAATCCGTGATTAACCCCCGGATAGATATACGCCTCATAAACCTTATTATTGGCTTTCAACGCCGCCTCGTA  >  minE/2009663‑2009777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A