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	2,301,495	T→C	61.9%	G192G (GGA→GGG)	metL ←	fused aspartokinase II and homoserine dehydrogenase II

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,301,495	0	T	C	61.9%	27.8 / 33.2	55	G192G (GGA→GGG)	metL	fused aspartokinase II and homoserine dehydrogenase II
Reads supporting (aligned to +/- strand): ref base T (10/11); new base C (9/25); total (19/36)
Fisher's exact test for biased strand distribution p-value = 1.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

GGAATAGTCGGAACCGTTACGCCCCAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACCAGCAGCTGTTGCAGCAACGGGTAA  >  minE/2301432‑2301555

ggAATAGTCGGAACCGTTACGCCCCAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGt                                                         <  1:2074378/69‑1 (MQ=255)

ggAATAGTCGGAACCGTTACGCCCCAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGt                                                         <  1:1549309/69‑1 (MQ=255)

 gAATAGTCGGAACCGTTACGCCCCAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGt                                                         <  1:1237719/68‑1 (MQ=255)

   aTAGTCGGAACCGTTACGCCCCAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTcac                                                      <  1:367138/69‑1 (MQ=255)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1524888/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:2163715/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1948303/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:3023791/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:3092698/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:3161553/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1800795/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1759019/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:3292625/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1718241/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:38958/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1596430/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:147971/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1468092/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:412468/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:603332/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1367037/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1276796/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1197532/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1160015/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:627549/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:949219/68‑1 (MQ=38)

    tAGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1033338/68‑1 (MQ=38)

     aGTCGGAACCGTTACGCCCAAGCAGCACCGTTTCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:1120727/67‑1 (MQ=38)

            aCCGTTACGCCCCAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACg                                             <  1:38998/69‑1 (MQ=255)

            aCCGTTACGCCCCAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACg                                             <  1:279600/69‑1 (MQ=255)

                      cccAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGa                                   <  1:1080236/69‑1 (MQ=255)

                      cccAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGa                                   <  1:1370139/69‑1 (MQ=255)

                      cccAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGa                                   <  1:137332/69‑1 (MQ=255)

                      cccAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGa                                   <  1:1411193/69‑1 (MQ=255)

                           cagcaCCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTg                              <  1:2933905/69‑1 (MQ=255)

                                  gTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACcagc                       >  1:2764215/1‑69 (MQ=255)

                                     tCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACCagcagc                    >  1:1866413/1‑69 (MQ=255)

                                     tCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACCagcagc                    >  1:66095/1‑69 (MQ=255)

                                     tCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACCagcagc                    >  1:1701493/1‑69 (MQ=255)

                                     tCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACCagcagc                    >  1:849182/1‑69 (MQ=255)

                                     tCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACCagcagc                    >  1:1749173/1‑69 (MQ=255)

                                     tCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACCagcagc                    >  1:890958/1‑69 (MQ=255)

                                     tCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACCagcagc                    >  1:1926906/1‑69 (MQ=255)

                                     tCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACCagcagc                    >  1:2623304/1‑69 (MQ=255)

                                     tCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTT‑CCCGGATGTTGCACCAGCAGCt                   >  1:183073/1‑69 (MQ=255)

                                     tCACCGGCGTTGTTACGGCTGATAAACCCGGTcac                                                      <  1:2356031/35‑1 (MQ=37)

                                                        tGATAAACCCGGTCACCACCAGCCGTTTGCCCGGAt                                  >  1:2782110/1‑36 (MQ=21)

                                                        tGATAAACCCGGTCACCACCAGACGTTTGCCCGGATGTTGTACCAGTAGCTGTTGCAGCAACGGGTac  >  1:1089442/1‑67 (MQ=255)

                                                        tGATAAACCCGGTCACCACCAGACGTTTGCCCGGATGTTGTACCAGTAGCTGTTGCAGCAACGGGTac  >  1:2323829/1‑67 (MQ=255)

                                                        tGATAAACCCGGTCACCACCAGACGTTTGCCCGGATGTTGTACCAGTAGCTGTTGCAGCAACGGGTac  >  1:773682/1‑67 (MQ=255)

                                                        tGATAAACCCGGTCACCACCAGACGTTTGCCCGGATGTTGTACCAGTAGCTGTTGCAGCAACGGGTac  >  1:1147370/1‑67 (MQ=255)

                                                        tGATAAACCCGGTCACCACCAGACGTTTGCCCGGATGTTGTACCAGTAGCTGTTGCAGCAACGGGTac  >  1:1665312/1‑67 (MQ=255)

                                                        tGATAAACCCGGTCACCACCAGACGTTTGCCCGGATGTTGTACCAGTAGCTGTTGCAGCAACGGGTac  >  1:348318/1‑67 (MQ=255)

                                                        tGATAAACCCGGTCACCACCAGACGTTTGCCCGGATGTTGTACCAGTAGCTGTTGCAGCAACGGGTac  >  1:1912541/1‑67 (MQ=255)

                                                        tGATAAACCCGGTCACCACCAGACGTTTGCCCGGATGTTGTACCAGTAGCTGTTGCAGCAACGGGTac  >  1:2986602/1‑67 (MQ=255)

GGAATAGTCGGAACCGTTACGCCCCAGCAGCACCGTTTCACCGGCGTTGTTGCGGCTGATAAATCCGGTCACCACCAGACGTTTGCCCGGATGTTGCACCAGCAGCTGTTGCAGCAACGGGTAA  >  minE/2301432‑2301555

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