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	985,963	A→G	60.7%	L68L (CTA→CTG)	ynfE →	oxidoreductase subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	985,963	0	A	G	60.7%	29.0 / 38.7	61	L68L (CTA→CTG)	ynfE	oxidoreductase subunit
Reads supporting (aligned to +/- strand): ref base A (14/10); new base G (10/27); total (24/37)
Fisher's exact test for biased strand distribution p-value = 1.81e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.26e-01

AGGCCCGCGAAAAAGTGGTCTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGCAACC  >  minE/985896‑986030

aGGCCCGCGAAAAAGTGGTCTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTa                                                                     <  1:379216/68‑1 (MQ=255)

      gcgAAAAAGTGGTCTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTa                                                              <  1:312552/69‑1 (MQ=255)

      gcgAAAAAGTGGTCTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTa                                                              <  1:1643284/69‑1 (MQ=255)

      gcgAAAAAGTGGTCTGGGGTGCCTGCTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTa                                                              <  1:1258598/69‑1 (MQ=255)

        gAAATAGTGGTCTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTa                                                              <  1:418805/67‑1 (MQ=255)

           aaaGTGGTCTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGGACTTCGTCTACATGTTAAAGAt                                                         <  1:1344882/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:2239720/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:1034536/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:2263725/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:2273103/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:2409537/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:2419168/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:250896/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:2567126/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:296917/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:2981982/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:595801/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:614462/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:632267/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:766490/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:878493/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:218905/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:1019602/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:1182767/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:1213094/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:124304/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:1274552/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:1604923/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:2229191/69‑1 (MQ=255)

                   cTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAA‑ATAATGAAGt                                                 <  1:1718070/68‑1 (MQ=255)

                   cTGGGGCGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:2056215/69‑1 (MQ=255)

                                tCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTAAAGATAATGAAGTGACCTGGGTGGaa                                    >  1:3067569/1‑69 (MQ=255)

                                tCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTAAAGATAATGAAGTGACCTGGGTAGaa                                    >  1:728206/1‑69 (MQ=255)

                                 ccGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTAAAGATAATGa                                                    <  1:2290161/52‑1 (MQ=255)

                                 ccGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTAAAGATAATGa                                                    <  1:460739/52‑1 (MQ=255)

                                 ccGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTAAAGATAATGa                                                    <  1:3383894/52‑1 (MQ=255)

                                 ccGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTAAAGATAATGa                                                    <  1:3254620/52‑1 (MQ=255)

                                 ccGTCAACTGTGGTAGCCGCTATGCACTTCGTCTACATGTTAAAGATAATGa                                                    <  1:2847286/52‑1 (MQ=255)

                                          gtgtTAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:1867513/46‑1 (MQ=255)

                                              tAGCCGCTGTGCACTTCGTCTGCGTGTTAAAGATAATGAAGTGa                                               >  1:3371432/1‑44 (MQ=38)

                                              tAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGTGAc                                              >  1:1593668/1‑45 (MQ=255)

                                              tAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGTGAc                                              >  1:1035569/1‑45 (MQ=255)

                                              tAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGTGAc                                              >  1:1060478/1‑45 (MQ=255)

                                              tAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGTGAc                                              >  1:2479724/1‑45 (MQ=255)

                                              tAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGTGAc                                              >  1:421688/1‑45 (MQ=255)

                                              tAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGTGAc                                              >  1:2615148/1‑45 (MQ=255)

                                              tAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGTGAc                                              >  1:3226897/1‑45 (MQ=255)

                                              tAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGTGAc                                              >  1:1486062/1‑45 (MQ=255)

                                              tAGCCGCTGTGCACTTCGTCTGCATGTTAAAGATAATGAAGTGAc                                              >  1:1524697/1‑45 (MQ=255)

                                                     tgtgCACTTCGTCTGCATGTTAAAGATAATGAAGt                                                 <  1:2354002/35‑1 (MQ=255)

                                                              cGTCTACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACgg       >  1:2885995/1‑68 (MQ=255)

                                                              cGTCTACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGc      >  1:3302610/1‑69 (MQ=255)

                                                              cGTCTACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGc      >  1:268967/1‑69 (MQ=255)

                                                              cGTCTACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGc      >  1:3027758/1‑69 (MQ=255)

                                                              cGTCTACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGc      >  1:2402203/1‑69 (MQ=255)

                                                              cGTCTACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGc      >  1:2433827/1‑69 (MQ=255)

                                                              cGTCTACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGc      >  1:2053017/1‑69 (MQ=255)

                                                                  tACATGTTAAAGATAATGAAGTGACCTGGGTGGaa                                    >  1:2364147/1‑35 (MQ=255)

                                                                  tACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGCAAcc  >  1:266492/1‑69 (MQ=255)

                                                                  tACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGCAAcc  >  1:433221/1‑69 (MQ=255)

                                                                  tACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGCAAcc  >  1:2977413/1‑69 (MQ=255)

                                                                  tACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGCAAc   >  1:2602810/1‑68 (MQ=255)

AGGCCCGCGAAAAAGTGGTCTGGGGTGCCTGTTCCGTCAACTGTGGTAGCCGCTGTGCACTTCGTCTACATGTTAAAGATAATGAAGTGACCTGGGTGGAAACTGACAATACCGGCAGCGATGAGTACGGCAACC  >  minE/985896‑986030

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