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	958,752	C→A	60.5%	A518A (GCG→GCT)	pqqL ←	predicted peptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	958,752	0	C	A	60.5%	15.1 / 38.6	43	A518A (GCG→GCT)	pqqL	predicted peptidase
Reads supporting (aligned to +/- strand): ref base C (6/11); new base A (11/15); total (17/26)
Fisher's exact test for biased strand distribution p-value = 7.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

GGATTTTGCCAGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCTACTGTTAACGATAAATTTCTGC  >  minE/958695‑958819

ggATTTTGCCAGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTc                                                          <  1:1269345/69‑1 (MQ=255)

 gATTTTGCCAGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTc                                                          <  1:2774277/68‑1 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTgctgct                                                 >  1:1070955/1‑68 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTGCTGCTa                                                >  1:1070887/1‑69 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTGCTGCTa                                                >  1:832269/1‑69 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTGCTGCTa                                                >  1:1123530/1‑69 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTGCTGCTa                                                >  1:711603/1‑69 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTGCTGCTa                                                >  1:1253064/1‑69 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTGCTGCTa                                                >  1:2155973/1‑69 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTGCTGCTa                                                >  1:2635707/1‑69 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTGCTGCTa                                                >  1:3376069/1‑69 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTGCTGCTa                                                >  1:3310081/1‑69 (MQ=255)

          aGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCAGCCAGCGTTTCTTTGCTGCTa                                                >  1:3112474/1‑69 (MQ=255)

              tAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAAttt                                            >  1:2060508/1‑69 (MQ=255)

                aCCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCCGCCATCGTTTCTTTGCTGCTAATTTcc                                          >  1:477276/1‑69 (MQ=255)

                aCCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTcc                                          >  1:3103160/1‑69 (MQ=255)

                aCCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTcc                                          >  1:667748/1‑69 (MQ=255)

                   cTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGcc                                       <  1:3226323/69‑1 (MQ=255)

                                aaaGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCg                           >  1:2438817/1‑68 (MQ=255)

                                 aaGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTc                         <  1:791879/69‑1 (MQ=255)

                                 aaGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTc                         <  1:1132232/69‑1 (MQ=255)

                                 aaGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTc                         <  1:1537699/69‑1 (MQ=255)

                                 aaGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTc                         <  1:3292003/69‑1 (MQ=255)

                                 aaGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTc                         <  1:3077474/69‑1 (MQ=255)

                                  aGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCt                        <  1:1337265/69‑1 (MQ=255)

                                  aGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCt                        <  1:1544029/69‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:2053172/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:902215/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:1121725/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:629941/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:3340857/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:3296292/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:1902900/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:2104353/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:2349001/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:1048828/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:2517871/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:2967215/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:2675018/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:2759683/68‑1 (MQ=255)

                                                   aTTCTCAGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCAGCGTCTACTGTTAACGATAAAt        <  1:169600/68‑1 (MQ=255)

                                                    ttCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCt                        <  1:1603637/51‑1 (MQ=255)

                                                     tctcCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCTACTGTTAACGATAAATTTc     >  1:2695626/1‑69 (MQ=255)

                                                        ccGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCTACTGTTAACGATAAATTTCTg   >  1:2282691/1‑68 (MQ=255)

                                                        ccGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCTACTGTTAACGATAAATTTCTGc  >  1:3308305/1‑69 (MQ=255)

                                                        ccGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCTACTGTTAACGATAAATTTCTGc  >  1:1450348/1‑69 (MQ=255)

                                                        ccGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCTACTGTTAACGATAAATTTCTGc  >  1:1305016/1‑69 (MQ=255)

                                                        ccGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCTACTGTTAACGATAAATTTCTGc  >  1:1592240/1‑69 (MQ=255)

                                                        ccGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCTACTGTTAACGATAAATTTCTGc  >  1:2286568/1‑69 (MQ=255)

GGATTTTGCCAGAATAACCCTGGCACCATTGGAAAGTGTTAATGATGTCAGATTCTCCGCCAGCGTTTCTTTGCTGCTAATTTCCGCCTGTGGGTCTGCGTCTACTGTTAACGATAAATTTCTGC  >  minE/958695‑958819

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