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
A1 F28 I2 R2	356	55.1	4139924	95.4%	3949487	63.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,985,254	G→A	S251N (AGC→AAC)	yqeG →	predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,985,254	0	G	A	94.7%	167.1 / 1.2	57	S251N (AGC→AAC)	yqeG	predicted transporter
Reads supporting (aligned to +/- strand): ref base G (0/3); new base A (24/30); total (24/33)
Fisher's exact test for biased strand distribution p-value = 2.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-01

AAAAAATTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAGCTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAAAGAAGAAGGGGT  >  W3110S.gb/2985194‑2985308

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:2015778/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:369126/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:3519831/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:3496532/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:3486003/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:3219697/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:3784351/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:3804500/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:1903828/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:442802/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:1549988/71‑1 (MQ=255)

aaaaaaTTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:1216061/71‑1 (MQ=255)

            aaGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:676029/59‑1 (MQ=255)

            aaGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:2219024/59‑1 (MQ=255)

            aaGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:3139528/59‑1 (MQ=255)

            aaGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCtt                                              <  1:2770641/59‑1 (MQ=255)

              gTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCttt                                             >  1:3560271/1‑58 (MQ=255)

              gTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTc                                            >  1:1788626/1‑59 (MQ=255)

              gTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTc                                            >  1:1189627/1‑59 (MQ=255)

              gTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTc                                            >  1:3070998/1‑59 (MQ=255)

                 gCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGta                             <  1:1127887/71‑1 (MQ=255)

                 gCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGta                             <  1:3624769/71‑1 (MQ=255)

                 gCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGta                             <  1:3742511/71‑1 (MQ=255)

                 gCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGta                             <  1:1424824/71‑1 (MQ=255)

                 gCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGta                             <  1:546850/71‑1 (MQ=255)

                      tctcATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTcc                                      <  1:1251647/57‑1 (MQ=255)

                      tctcATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTcc                                      <  1:456697/57‑1 (MQ=255)

                        tcatcaTCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCAc                                    >  1:3104071/1‑57 (MQ=255)

                        tcatcaTCTGCATAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCAc                                    >  1:402027/1‑57 (MQ=255)

                                   aTAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTTTTCCACCTTCGTATATTGAAGCTGCTAaaga           <  1:1241239/71‑1 (MQ=255)

                                   aTAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaaga           <  1:3773303/71‑1 (MQ=255)

                                   aTAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaaga           <  1:382259/71‑1 (MQ=255)

                                   aTAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaaga           <  1:4110803/71‑1 (MQ=255)

                                   aTAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaaga           <  1:1716085/71‑1 (MQ=255)

                                    tAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaaga           <  1:600470/70‑1 (MQ=255)

                                    tAAGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaaga           <  1:513493/70‑1 (MQ=255)

                                      aGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaagaa          >  1:689329/1‑69 (MQ=255)

                                      aGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaagaa          >  1:3510562/1‑69 (MQ=255)

                                      aGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaagaa          >  1:1645948/1‑69 (MQ=255)

                                      aGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaagaa          >  1:1660856/1‑69 (MQ=255)

                                      aGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATT‑AAGCTGCTAaagaa          >  1:3654977/1‑68 (MQ=255)

                                      aGTGTACTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATAATGAAGCTGCTAaagaa          >  1:2342475/1‑69 (MQ=255)

                                      aGTGTACTGTTCTTTGTCTTTAACTGCCTGCATTCTATT‑CACCTTCGTATATTg                        >  1:3873808/1‑54 (MQ=255)

                                      aGTGTAATGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaagaa          >  1:3855246/1‑69 (MQ=255)

                                            cTGTTCTTTGTCTTTAGCTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAAAGAAGAAGGGGt  <  1:1165809/71‑1 (MQ=255)

                                            cTGTTCTTTGTCTTTAGCTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAAAGAAGAAGGGGt  <  1:1196838/71‑1 (MQ=255)

                                            cTGTTCTTTGTCTTTAGCTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAAAGAAGAAGGGGt  <  1:2872893/71‑1 (MQ=255)

                                            cTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGtata                           >  1:3833342/1‑46 (MQ=255)

                                            cTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGtata                           >  1:1863558/1‑46 (MQ=255)

                                            cTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGtata                           >  1:2666856/1‑46 (MQ=255)

                                            cTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAAAGAAGAAGGGGt  >  1:2660018/1‑71 (MQ=255)

                                            cTGTTCTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAAAGAAGAAGGGGt  >  1:1982094/1‑71 (MQ=255)

                                                 cTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaagaagaa       >  1:3841886/1‑61 (MQ=255)

                                                 cTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaagaagaa       >  1:189705/1‑61 (MQ=255)

                                                 cTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaagaagaa       >  1:1711352/1‑61 (MQ=255)

                                                 cTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaagaagaa       >  1:2747133/1‑61 (MQ=255)

                                                 cTTTGTCTTTAACTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAaagaagaa       >  1:3626627/1‑61 (MQ=255)

AAAAAATTATGAAAGTCGCTTATCTCATCATCTGCATAAGTGTACTGTTCTTTGTCTTTAGCTGCCTGCTTTCTATTCCACCTTCGTATATTGAAGCTGCTAAAGAAGAAGGGGT  >  W3110S.gb/2985194‑2985308

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