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	1,698,435	A→T	58.7%	Q105H (CAA→CAT)	csiE →	stationary phase inducible protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,698,435	0	A	T	58.7%	25.5 / 61.3	63	Q105H (CAA→CAT)	csiE	stationary phase inducible protein
Reads supporting (aligned to +/- strand): ref base A (9/17); new base T (20/17); total (29/34)
Fisher's exact test for biased strand distribution p-value = 1.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.73e-01

CAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAC  >  minE/1698367‑1698500

cAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCaa                                                                   <  1:926489/69‑1 (MQ=255)

cAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCaa                                                                   <  1:1926529/69‑1 (MQ=255)

cAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCaa                                                                   <  1:1860605/69‑1 (MQ=255)

cAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCaa                                                                   <  1:3358091/69‑1 (MQ=255)

cAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCaa                                                                   <  1:332048/69‑1 (MQ=255)

cAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCaa                                                                   <  1:1568594/69‑1 (MQ=255)

cAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCaa                                                                   <  1:2417968/69‑1 (MQ=255)

cAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCaa                                                                   <  1:2538076/69‑1 (MQ=255)

cAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCaa                                                                   <  1:3058574/69‑1 (MQ=255)

cAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCaa                                                                   <  1:296478/69‑1 (MQ=255)

    gTTTGTGTTTATTTCACTGGCTACGACGTGG‑TTCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCAc                                                              <  1:2641892/69‑1 (MQ=255)

     tttGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCAc                                                              <  1:3274585/69‑1 (MQ=255)

     tttGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCAc                                                              <  1:1469334/69‑1 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCAttt                                                                 >  1:412009/1‑63 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAcccc                                                           >  1:3177045/1‑69 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAcccc                                                           >  1:2337881/1‑69 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAcccc                                                           >  1:3360989/1‑69 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAcccc                                                           >  1:1952785/1‑69 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAcccc                                                           >  1:194029/1‑69 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAcccc                                                           >  1:294709/1‑69 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAcccc                                                           >  1:1648985/1‑69 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAcccc                                                           >  1:560106/1‑69 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAcccc                                                           >  1:609141/1‑69 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAcccc                                                           >  1:1444246/1‑69 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAccc                                                            >  1:914660/1‑68 (MQ=255)

        gtgtTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCAccc                                                            >  1:3091019/1‑68 (MQ=255)

                   aCTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAag                                                 <  1:796642/68‑1 (MQ=255)

                      ggCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTg                                             <  1:407501/69‑1 (MQ=255)

                      ggCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTg                                             <  1:2174630/69‑1 (MQ=255)

                      ggCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTg                                             <  1:708009/69‑1 (MQ=255)

                      ggCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTg                                             <  1:1920497/69‑1 (MQ=255)

                            gacgTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCACCCCCGCCCTGAAGAGt                                              >  1:2586310/1‑62 (MQ=255)

                            gacgTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCACCCCCGCCCTGAAGAGTg                                             >  1:789771/1‑63 (MQ=255)

                            gacgTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCACCCCCGCCCTGAAGAGTg                                             >  1:3072828/1‑63 (MQ=255)

                            gacgTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCACCCCCGCCCTGAAGAGTg                                             >  1:1367069/1‑63 (MQ=255)

                            gacgTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCACCCCCGCCCTGAAGAGTg                                             >  1:46895/1‑63 (MQ=255)

                            gacgTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCACCCCCGCCCTGAAGAGTg                                             >  1:3402969/1‑63 (MQ=255)

                            gacgTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCATTTCACCCCCGCCCTGAAGAGTg                                             >  1:1675296/1‑63 (MQ=255)

                            gacgTGGTTTCCGTCAGTGTCCGTCATTTATTACCAGCCATTTCACCCCCGCCCTGAAGAGTg                                             >  1:1060515/1‑63 (MQ=255)

                                    ttCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGa                                       <  1:2389294/61‑1 (MQ=255)

                                    ttCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGa                                       <  1:264696/61‑1 (MQ=255)

                                        gTCTGTGTCCGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTg                                             <  1:937717/51‑1 (MQ=255)

                                                 cGTCATTTATTACCAGCCAATTCACGCCCGCCCTg                                                    >  1:2762422/1‑35 (MQ=255)

                                                 cGTCATTTATTACCAGCCAATTCACCCCCGCCCTg                                                    >  1:2923333/1‑35 (MQ=255)

                                                 cGTCATTTATTACCAGCCAATTCACCCCCGCCCTg                                                    >  1:2130874/1‑35 (MQ=255)

                                                 cGTCATTTATTACCAGCCAATTCACCCCCGCCCTg                                                    >  1:1363345/1‑35 (MQ=255)

                                                 cGTCATTTATTACCAGCCAATTCACCCCCGCCCTg                                                    >  1:2492325/1‑35 (MQ=255)

                                                 cGTCATTTATTACCAGCCAATTCACCCCCGCCCTg                                                    >  1:2700393/1‑35 (MQ=255)

                                                 cGTCATTTATTACCAGCCAATTCACCCCCGCCCTg                                                    >  1:2768480/1‑35 (MQ=255)

                                                 cGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTa                  >  1:1020723/1‑69 (MQ=255)

                                                 cGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTa                  >  1:166586/1‑69 (MQ=255)

                                                       ttattaCCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACtttt            <  1:2790267/69‑1 (MQ=255)

                                                       ttattaCCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACtttt            <  1:2939166/69‑1 (MQ=255)

                                                       ttattaCCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACtttt            <  1:3331090/69‑1 (MQ=255)

                                                       ttattaCCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACtttt            <  1:2156127/69‑1 (MQ=255)

                                                       ttattaCCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACtttt            <  1:1451555/69‑1 (MQ=255)

                                                       ttattaCCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACtttt            <  1:513057/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:2905625/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:1046712/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:101917/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:1449208/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:746743/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:1533692/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:571027/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:1571374/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:488035/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:1597346/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:1720563/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:386969/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:2110231/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:2179342/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:2511520/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:3092340/69‑1 (MQ=255)

                                                                 ccATTTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAc  <  1:2555523/69‑1 (MQ=255)

CAACGTTTGTGTTTATTTCACTGGCTACGACGTGGTTTCCGTCTGTGTCCGTCATTTATTACCAGCCAATTCACCCCCGCCCTGAAGAGTGAACTGAAGCGGCGCGGAATTGCGCGTAACTTTTACGACGATAC  >  minE/1698367‑1698500

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