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	425,081	G→A	60.6%	C324C (TGC→TGT)	nagA ←	N‑acetylglucosamine‑6‑phosphate deacetylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	425,081	0	G	A	60.6%	28.0 / 43.4	66	C324C (TGC→TGT)	nagA	N‑acetylglucosamine‑6‑phosphate deacetylase
Reads supporting (aligned to +/- strand): ref base G (22/4); new base A (25/15); total (47/19)
Fisher's exact test for biased strand distribution p-value = 9.35e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTCAACGCCAATCGCACGCGCCGGATAGAGCGTCGCCATACGTAGCACTTCATCCAGTGCGATACCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTT  >  minE/425014‑425146

tctcAACGCCAATCGCACGCGCCGGATAGAGCGTCGCCATACGTAGCACTTCATCCAGTGCGATACCGc                                                                  >  1:2662686/1‑69 (MQ=255)

tctcAACGCCAATCGCACGCGCCGGATAGAGCGTCGCCATACGTAGCACTTCATCCAGTGCGATACCGc                                                                  >  1:600556/1‑69 (MQ=255)

tctcAACGCCAATCGCACGCGCCGGATAGAGCGTCGCCATACGTAGCACTTCATCCAGTGCGATACCGc                                                                  >  1:2670625/1‑69 (MQ=255)

tctcAACGCCAATCGCACGCGCCGGATAGAGCGTCGCCATACGTAGCACTTCATCCAGTGCGATACCGc                                                                  >  1:2793548/1‑69 (MQ=255)

tctcAACGCCAATCGCACGCGCCGGATAGAGCGTCGCCATACGTAGCACTTCATCCAGTGCGATACCGc                                                                  >  1:1539249/1‑69 (MQ=255)

tctcAACGCCAATCGCACGCGCCGGATAGAGCGTCGCCATACGTAGCACTTCATCCAGTGCGATACCGc                                                                  >  1:3217111/1‑69 (MQ=255)

                                 tCGCCATACGTAGCACTTCATCCAGTGCGATACCGCAATGTTCGACCAGATTACGCACGCCTTCAATCa                                 <  1:2319133/69‑1 (MQ=255)

                                         cGTAGCACTTCATCCAGTGCGATACCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:83533/1‑69 (MQ=255)

                                         cGTAGCACTTCATCCAGTGCGATACCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:3241958/1‑69 (MQ=255)

                                         cGTAGCACTTCATCCAGAGCGATACCGCAATGTTCGACCAGATTACGCGCGCCTTCAATCATGGTTaa                          >  1:3023461/1‑68 (MQ=255)

                                             gCACTTCATCGAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:3082088/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:3331825/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:3119637/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:3038038/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:3388134/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:2876797/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:1851040/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:1334636/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:2750953/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:567470/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:2134267/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:854605/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:2522625/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATg                     <  1:906268/69‑1 (MQ=255)

                                             gCACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGAACGCCTTCAATCATGGTTAAGGATg                     <  1:254418/69‑1 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGCTTACGCACGCCTTCAATCATGGTTAAg                         >  1:1059954/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTacgctc                                            >  1:2192020/1‑43 (MQ=38)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGGCTTCAATCATGGTTAAg                         >  1:1735871/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGt                             >  1:115279/1‑60 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:1437689/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:960786/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:105031/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:802624/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:53472/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:411799/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:3409918/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:1410669/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:1413497/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:2320347/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:16756/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:1691086/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:1818816/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:2418755/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:1857121/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:2421706/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:2516016/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:1978365/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:2271043/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAg                         >  1:2146735/1‑64 (MQ=255)

                                              cACTTCATCCAGTGCGATACCACAATGTTCGACCAGATTACGCACGCCTTCAATAATGGTTAAg                         >  1:193450/1‑64 (MQ=255)

                                               aCTTCATCCAGTGCGATACCGCAATGTTCGACCAGATTACGCAGGCCTTCAATCATGGTTAAGGATGa                    <  1:3363449/68‑1 (MQ=255)

                                               aCTTCATCCAGTGCGATACCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGa                    <  1:318724/68‑1 (MQ=255)

                                                        tgTGCGATACCGCATTGTTCGACCTGATTACGCACGGCTTCAATCATGGTTAAGGATGa                    <  1:2791104/58‑1 (MQ=255)

                                                            cGATACCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTAc      >  1:608554/1‑69 (MQ=255)

                                                            cGATACCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTAc      >  1:1278904/1‑69 (MQ=255)

                                                                aCCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGtt  >  1:703954/1‑69 (MQ=255)

                                                                aCCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGtt  >  1:2322422/1‑69 (MQ=255)

                                                                aCCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGtt  >  1:66228/1‑69 (MQ=255)

                                                                aCCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGtt  >  1:1690625/1‑69 (MQ=255)

                                                                aCCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGt   >  1:2976529/1‑68 (MQ=255)

                                                                 ccGCAATGTTCGACCAGATTACGCACGCCTTCAAt                                   >  1:1260740/1‑35 (MQ=255)

                                                                 ccGCAATGTTCGACCAGATTACGCACGCCTTCAAt                                   >  1:3422715/1‑35 (MQ=255)

                                                                 ccGCAATGTTCGACCAGATTACGCACGCCTTCAAt                                   >  1:3391198/1‑35 (MQ=255)

                                                                 ccGCAATGTTCGACCAGATTACGCACGCCTTCAAt                                   >  1:1230270/1‑35 (MQ=255)

                                                                 ccGCAATGTTCGACCAGATTACGCACGCCTTCAAt                                   >  1:3325210/1‑35 (MQ=255)

                                                                 ccGCAATGTTCGACCAGATTACGCACGCCTTCAAt                                   >  1:1504696/1‑35 (MQ=255)

TCTCAACGCCAATCGCACGCGCCGGATAGAGCGTCGCCATACGTAGCACTTCATCCAGTGCGATACCGCAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTT  >  minE/425014‑425146

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