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	2,131,391	A→G	43.2%	I519I (ATT→ATC)	deaD ←	ATP‑dependent RNA helicase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,131,391	0	A	G	43.2%	17.2 / 56.8	74	I519I (ATT→ATC)	deaD	ATP‑dependent RNA helicase
Reads supporting (aligned to +/- strand): ref base A (26/16); new base G (13/19); total (39/35)
Fisher's exact test for biased strand distribution p-value = 1.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.56e-01

CACTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATGACGAACTTCAACACC  >  minE/2131325‑2131456

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:900915/69‑1 (MQ=255)

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:891533/69‑1 (MQ=255)

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:710406/69‑1 (MQ=255)

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:2995529/69‑1 (MQ=255)

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:3096124/69‑1 (MQ=255)

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:1943996/69‑1 (MQ=255)

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:3108008/69‑1 (MQ=255)

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:3233481/69‑1 (MQ=255)

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:144271/69‑1 (MQ=255)

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:3271565/69‑1 (MQ=255)

caCTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGAt                                                                 <  1:1437843/69‑1 (MQ=255)

       cccGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACg                                                           <  1:1724096/68‑1 (MQ=255)

        ccGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACg                                                           <  1:3321860/67‑1 (MQ=255)

            cATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     <  1:2070438/69‑1 (MQ=255)

            cATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     <  1:2516424/69‑1 (MQ=255)

            cATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     <  1:354247/69‑1 (MQ=255)

            cATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     <  1:2896612/69‑1 (MQ=255)

            cATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     <  1:286116/69‑1 (MQ=255)

            cATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     <  1:1177544/69‑1 (MQ=255)

            cATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     <  1:1450946/69‑1 (MQ=255)

            cATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     <  1:1531143/69‑1 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGAt                                                  >  1:127786/1‑68 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:639830/1‑69 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:2488464/1‑69 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:1280148/1‑69 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:826812/1‑69 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:763241/1‑69 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:2003011/1‑69 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:1877624/1‑69 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:622867/1‑69 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:1743638/1‑69 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:1742406/1‑69 (MQ=255)

                ccTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAAAAGCTTGATGTTACCAATGTAACGGCTGCTGATg                                                 >  1:523368/1‑69 (MQ=255)

                           ttCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGtt                                      <  1:720890/69‑1 (MQ=255)

                           ttCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGtt                                      <  1:1613540/69‑1 (MQ=255)

                            tCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGtt                                      >  1:1159534/1‑68 (MQ=255)

                            tCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGtt                                      >  1:1117737/1‑68 (MQ=255)

                            tCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGtt                                      >  1:201556/1‑68 (MQ=255)

                            tCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGtt                                      >  1:3266474/1‑68 (MQ=255)

                            tCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGtt                                      >  1:3390754/1‑68 (MQ=255)

                               aTGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGc                                   <  1:822162/68‑1 (MQ=255)

                               aTGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGc                                   <  1:3329107/68‑1 (MQ=255)

                               aTGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGc                                   <  1:2897510/68‑1 (MQ=255)

                               aTGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGc                                   <  1:1005559/68‑1 (MQ=255)

                               aTGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGc                                   <  1:1873178/68‑1 (MQ=255)

                                tggtggAGTGAGAAGCAAACAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGc                                   <  1:919329/67‑1 (MQ=255)

                                tggtggAGTGAGAAGCAAACAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGc                                   <  1:283138/67‑1 (MQ=255)

                                     gAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCa                            <  1:983944/69‑1 (MQ=255)

                                          agaAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     >  1:1885921/1‑39 (MQ=255)

                                          agaAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     >  1:926344/1‑39 (MQ=255)

                                          agaAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     >  1:154555/1‑39 (MQ=255)

                                          agaAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     >  1:1726932/1‑39 (MQ=255)

                                          agaAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     >  1:1812796/1‑39 (MQ=255)

                                          agaAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     >  1:2413482/1‑39 (MQ=255)

                                          agaAGCAAACAGCTTGATGTTACCAATGTAACGgctgct                                                     >  1:2581528/1‑39 (MQ=255)

                                          agaAGCAAACAGCTTGATGTTACCAATGTAACGgctgc                                                      >  1:2137817/1‑38 (MQ=255)

                                          agaAGCAAACAGCTTGATGTTA‑CAATGTAACGgctgct                                                     >  1:2029726/1‑38 (MQ=255)

                                             atcAAACCGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGa                     <  1:328056/66‑1 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:2663457/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:2078601/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:2617440/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:3021606/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:1003560/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:898524/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:1269406/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:1340648/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:1363946/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:3132562/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:1906682/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:195716/1‑68 (MQ=255)

                                                 aaCAGCTTGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATg                 >  1:1967817/1‑68 (MQ=255)

                                                        tGATGTTACCGATGTAACGGCTGCTGATGTCGCCTTCGTTAGc                                   <  1:1018003/43‑1 (MQ=255)

                                                               aCCAATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATGACGAACTTCAACAcc  <  1:3150810/69‑1 (MQ=255)

                                                               aCCAATGTAACGGCTGCTGATGTAGCCTTCGTTAGCAATCGCACCAACGATATGACGAACTTCAACAcc  <  1:1589211/69‑1 (MQ=255)

CACTTCACCCGGCATACCTTTCGGCAGTTCGATGGTGGAGTGAGAAGCAAACAGCTTGATGTTACCAATGTAACGGCTGCTGATGTCGCCTTCGTTAGCAATCGCACCAACGATATGACGAACTTCAACACC  >  minE/2131325‑2131456

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