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 F8 I0 R2	422	46.8	3726540	94.7%	3529033	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	249,599	A→G	31.0%	pseudogene (472/1713 nt)	fhiA ←	ECK0230:JW5811:b0229; flagellar system protein, promoterless fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	249,599	0	A	G	31.0%	33.4 / 21.3	29	pseudogene (472/1713 nt)	fhiA	ECK0230:JW5811:b0229; flagellar system protein, promoterless fragment
Reads supporting (aligned to +/- strand): ref base A (9/11); new base G (5/4); total (14/15)
Fisher's exact test for biased strand distribution p-value = 7.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

GCAGGTGCGGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGA  >  W3110S.gb/249533‑249667

gCAGGTGCGGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACggg                                                                  <  1:279353/71‑1 (MQ=255)

gCAGGTGCGGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACggg                                                                  <  1:2714930/71‑1 (MQ=255)

gCAGGTGCGGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACggg                                                                  <  1:2580627/71‑1 (MQ=255)

            ttCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCcagc                                                         <  1:969166/68‑1 (MQ=255)

             tCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCcagc                                                         <  1:2079487/67‑1 (MQ=255)

              cccGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGGCGGGCTTGCCAGCAGCTg                                                    >  1:2898907/1‑71 (MQ=255)

              cccGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTg                                                    >  1:1520407/1‑71 (MQ=255)

                         cGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGt                                         <  1:3198660/71‑1 (MQ=255)

                                aCGAACATAATCCCGGTGGCGGTGTAGAGCACCGGCGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGc                                  <  1:2034045/71‑1 (MQ=255)

                                aCGAACATAATCCCGGTGGCGGTGTAGAGCACCGGCGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGc                                  <  1:2747834/71‑1 (MQ=255)

                                   aaCATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGat                               <  1:1842429/71‑1 (MQ=255)

                                   aaCATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGat                               <  1:1035689/71‑1 (MQ=255)

                                       tAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACg                                              <  1:3561105/52‑1 (MQ=255)

                                       tAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACg                                              <  1:2080104/52‑1 (MQ=255)

                                       tAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACg                                              <  1:2826042/52‑1 (MQ=255)

                                                       gtAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcgc           >  1:3166509/1‑71 (MQ=255)

                                                       gtAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcgc           >  1:1743226/1‑71 (MQ=255)

                                                       gtAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcgc           >  1:599541/1‑71 (MQ=255)

                                                       gtAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcgc           >  1:310849/1‑71 (MQ=255)

                                                       gtAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcgc           >  1:2281241/1‑71 (MQ=255)

                                                       gtAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCAGTTGTCGCTGAcg            >  1:351986/1‑70 (MQ=255)

                                                        tAGAGCACCGGCGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcgcg          <  1:115170/71‑1 (MQ=255)

                                                        tAGAGCACCGGCGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGAcgcg          <  1:3327929/71‑1 (MQ=255)

                                                          gagCACCGGCGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCg                  >  1:3655902/1‑61 (MQ=255)

                                                          gagCACCGGCGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCggg        >  1:2524094/1‑71 (MQ=255)

                                                          gagCACCGGCGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCggg        >  1:1244124/1‑71 (MQ=255)

                                                          gagCACCGGCGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCggg        >  1:697477/1‑71 (MQ=255)

                                                             cACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGa     >  1:2118912/1‑71 (MQ=255)

                                                                 gACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGa  >  1:2154259/1‑70 (MQ=255)

GCAGGTGCGGCATTCCCGGTACCACCGCCAGCACGAACATAATCCCGGTGGCGGTGTAGAGCACCGACGGGCTTGCCAGCAGCTGGTTACGCACGTCATGGGCGATATCGCCGTTGTCGCTGACGCGGGTGACGA  >  W3110S.gb/249533‑249667

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