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	2,541,664	G→A	E129K (GAA→AAA)	crr →	glucose‑specific enzyme IIA component of PTS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,541,664	0	G	A	88.0%	137.6 / 10.2	50	E129K (GAA→AAA)	crr	glucose‑specific enzyme IIA component of PTS
Reads supporting (aligned to +/- strand): ref base G (2/4); new base A (16/28); total (18/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAA  >  W3110S.gb/2541599‑2541717

ttGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGaaa                                                     >  1:719067/1‑68 (MQ=255)

ttGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGaaa                                                     >  1:1388689/1‑68 (MQ=255)

ttGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGaaa                                                     >  1:1543102/1‑68 (MQ=255)

  gCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAgaga                                                 >  1:62558/1‑70 (MQ=255)

  gCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAgaga                                                 >  1:860196/1‑70 (MQ=255)

  gCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAagag                                                  >  1:375708/1‑69 (MQ=255)

  gCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAgaga                                                 >  1:3939233/1‑70 (MQ=255)

  gCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAgaga                                                 >  1:1340861/1‑70 (MQ=255)

        gaagGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAag                                                    <  1:2609665/61‑1 (MQ=255)

        gaagGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAag                                                    <  1:176497/61‑1 (MQ=255)

        gaagGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAag                                                    <  1:2469160/61‑1 (MQ=255)

        gaagGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAag                                                    <  1:503040/61‑1 (MQ=255)

        gaagGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAag                                                    <  1:3644875/61‑1 (MQ=255)

        gaagGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGcc                                            >  1:1556571/1‑69 (MQ=255)

        gaagGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGcc                                            >  1:2296677/1‑69 (MQ=255)

             tCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAag                                                    <  1:3959138/56‑1 (MQ=255)

               aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTAc                                    <  1:2755145/70‑1 (MQ=255)

               aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTAc                                    <  1:526470/70‑1 (MQ=255)

                gcgcGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTAc                                    <  1:546298/69‑1 (MQ=255)

                 cgcgTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAgaga                                                 >  1:2062489/1‑55 (MQ=255)

                    gTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGAc                              <  1:1932940/71‑1 (MQ=255)

                    gTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGAc                              <  1:1371711/71‑1 (MQ=255)

                     tGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGAc                              <  1:1888073/70‑1 (MQ=255)

                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGGCTcc                           >  1:3719728/1‑71 (MQ=255)

                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTcc                           >  1:2367289/1‑71 (MQ=255)

                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTcc                           >  1:662072/1‑71 (MQ=255)

                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTcc                           >  1:2871158/1‑71 (MQ=255)

                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTcc                           >  1:1067945/1‑71 (MQ=255)

                       aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTc                            >  1:549120/1‑70 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgtt                    <  1:1254103/71‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgtt                    <  1:685545/71‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgtt                    <  1:3201690/71‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgtt                    <  1:2186491/71‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgt                     <  1:1685050/70‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgt                     <  1:184280/70‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgt                     <  1:1951778/70‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgt                     <  1:1717640/70‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgt                     <  1:734174/70‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgt                     <  1:2601666/70‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgt                     <  1:3920907/70‑1 (MQ=255)

                              gCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgt                     <  1:3912478/70‑1 (MQ=255)

                                      gTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa            >  1:3900159/1‑71 (MQ=255)

                                      gTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa            >  1:2237847/1‑71 (MQ=255)

                                      gTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa            >  1:2731131/1‑71 (MQ=255)

                                      gTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa            >  1:2823050/1‑71 (MQ=255)

                                         aTTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTa                                     <  1:2667570/43‑1 (MQ=255)

                                         aTTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTa                                     <  1:2297323/43‑1 (MQ=255)

                                         aTTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTa                                     <  1:3612448/43‑1 (MQ=255)

                                         aTTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTa                                     <  1:1764586/43‑1 (MQ=255)

                                                 tGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGaa  <  1:231135/70‑1 (MQ=255)

                                                 tGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGaa  <  1:3066065/70‑1 (MQ=255)

                                                 tGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGaa  <  1:3228517/70‑1 (MQ=255)

                                                  gATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGaa  <  1:2110507/69‑1 (MQ=255)

TTGCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAA  >  W3110S.gb/2541599‑2541717

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A