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 R2	230	93.6	4701257	96.3%	4527310	61.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,960,872	G→A	52.2%	intergenic (+322/+98)	yjjV → / ← yjjW	predicted DNase/predicted pyruvate formate lyase activating enzyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,960,872	0	G	A	52.2%	‑6.1 / 28.2	23	intergenic (+322/+98)	yjjV/yjjW	predicted DNase/predicted pyruvate formate lyase activating enzyme
Reads supporting (aligned to +/- strand): ref base G (7/4); new base A (4/8); total (11/12)
Fisher's exact test for biased strand distribution p-value = 2.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGCGACGCTTGTCGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTATCAGGCCTACAAGTCTGT  >  minE/2960802‑2960942

aTGCGACGCTTGTCGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTcgcg                                                                        <  1:3555367/71‑1 (MQ=255)

    gACGCTTGTCGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGcgccg                                                                     >  1:3320024/1‑70 (MQ=255)

                gTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATACGGCGTTCGCGCCGCATCCGGCAGTTg                                                        >  1:3348384/1‑71 (MQ=21)

                gTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCACCGCATCCGGCAGTTg                                                        <  1:1302991/71‑1 (MQ=21)

                     aTCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCAGTTGGCGca                                                   >  1:4440693/1‑71 (MQ=34)

                     aTCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCACCGCATCCGGCAGTTGgcgc                                                    <  1:3419196/70‑1 (MQ=25)

                      tCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCACCGCATCCGGCAGTTGGCGcac                                                  <  1:4613820/71‑1 (MQ=21)

                      tCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCACCGCATCCGGCAGTTGGCGca                                                   <  1:2703058/70‑1 (MQ=25)

                        aTGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCAGTTGGCGCACaa                                                >  1:486007/1‑71 (MQ=34)

                         tGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCAGTT‑GCGCACAATg                                              <  1:2276634/71‑1 (MQ=255)

                               cAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCAGTTGGCGCACAATGc                                             >  1:1131422/1‑67 (MQ=35)

                               cAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCAGTTGGCGCACAATGCCTGa                                         >  1:2694000/1‑71 (MQ=34)

                                  gTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGc                                      >  1:2277240/1‑71 (MQ=34)

                                    ttGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCACCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGa                                    >  1:2259530/1‑71 (MQ=21)

                                       tgCCGAACCGTAGGCCGGATAAGGCGTTCGCACCGCATc                                                                 >  1:1685053/1‑39 (MQ=255)

                                         ccGAACCGTAGGCCGGATAAGGCGTTCGCACCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCtt                               <  1:4183764/71‑1 (MQ=21)

                                           gAACCGTAGGCCGGATAAGGCGTTCGCACCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTg                              <  1:2544398/70‑1 (MQ=25)

                                            aaCCGTAGGCCGGATAAGGCGTTCGCACCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGAc                            <  1:1714494/71‑1 (MQ=255)

                                                 tAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTc                       <  1:2242374/71‑1 (MQ=39)

                                                    gCCGGATAAGGCGTTCGCACCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTa                    <  1:3472085/71‑1 (MQ=255)

                                                     ccGGATAAGGCGTTCGCGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTAt                   <  1:1710864/71‑1 (MQ=39)

                                                      cGGATAAGGCGTTCGCGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTAt                   <  1:4377803/70‑1 (MQ=40)

                                                        gATAAGGCGTTCGCACCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTATCa                 >  1:712797/1‑70 (MQ=255)

                                                          tAAGGCGTTCGCACCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTATCAGGc              >  1:4075436/1‑71 (MQ=255)

                                                           aaGGCGTTCGCGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTATCAGGcc             >  1:210371/1‑71 (MQ=255)

                                                                   cgcaCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTATCAGGCCTACAAGt      <  1:3348441/70‑1 (MQ=255)

                                                                   cgcaCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTATCAGGCCTACAAGTc     >  1:3535173/1‑71 (MQ=255)

                                                                    gcgcCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTATCAGGCCTACAAGTCt    >  1:3262006/1‑71 (MQ=40)

                                                                      gccgcATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTATCAGGCCTACAAGTCtgt  <  1:4028997/71‑1 (MQ=39)

ATGCGACGCTTGTCGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTGACGCGTCTTATCAGGCCTACAAGTCTGT  >  minE/2960802‑2960942

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