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	1,119,187	G→A	62.9%	H175H (CAC→CAT)	ydiV ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,119,187	0	G	A	62.9%	31.8 / 37.8	62	H175H (CAC→CAT)	ydiV	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (15/8); new base A (8/31); total (23/39)
Fisher's exact test for biased strand distribution p-value = 8.59e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

TGCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAC  >  minE/1119132‑1119242

tGCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgtt                                            >  1:3289900/1‑69 (MQ=255)

 gCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgttg                                           >  1:2143012/1‑69 (MQ=255)

 gCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgttg                                           >  1:3382611/1‑69 (MQ=255)

 gCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgttg                                           >  1:374708/1‑69 (MQ=255)

 gCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgttg                                           >  1:2997404/1‑69 (MQ=255)

 gCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgttg                                           >  1:2642883/1‑69 (MQ=255)

 gCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgttg                                           >  1:2074094/1‑69 (MQ=255)

 gCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgttg                                           >  1:1919407/1‑69 (MQ=255)

 gCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgttg                                           >  1:1740563/1‑69 (MQ=255)

 gCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgttg                                           >  1:919546/1‑69 (MQ=255)

 gCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATttgttg                                           >  1:1188441/1‑69 (MQ=255)

           gAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTGAtt                                                >  1:1569910/1‑54 (MQ=255)

           gAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATaaaa                                 >  1:2939738/1‑69 (MQ=255)

           gAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATaaaa                                 >  1:662953/1‑69 (MQ=255)

           gAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATaaaa                                 >  1:2171487/1‑69 (MQ=255)

           gAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATaaaa                                 >  1:1727404/1‑69 (MQ=255)

           gAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATaaaa                                 >  1:3084806/1‑69 (MQ=255)

           gAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATaaaa                                 >  1:1097490/1‑69 (MQ=255)

           gAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATaaaa                                 >  1:1093546/1‑69 (MQ=255)

                 tGCGCCTGGATCTCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:2080178/45‑1 (MQ=38)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:812302/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:477695/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:2828879/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:3294008/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:270232/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:2696953/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:1082939/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:2189240/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:1607468/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:1908084/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:2282588/45‑1 (MQ=255)

                 tGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGATGCGTg                                                   <  1:131567/45‑1 (MQ=255)

                         taTCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   >  1:1532431/2‑69 (MQ=255)

                         gATCGCACGAATAAACGGTTCGAAGGAGCGGTTCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   >  1:384838/1‑69 (MQ=255)

                         gATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   >  1:1712087/1‑69 (MQ=255)

                           tCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   <  1:1755626/67‑1 (MQ=255)

                           tCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   <  1:1380690/67‑1 (MQ=255)

                           tCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   <  1:426154/67‑1 (MQ=255)

                           tCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   <  1:3116244/67‑1 (MQ=255)

                           tCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   <  1:3012559/67‑1 (MQ=255)

                           tCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   <  1:825893/67‑1 (MQ=255)

                           tCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   <  1:1282001/67‑1 (MQ=255)

                           tCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCAt                   <  1:2462323/67‑1 (MQ=255)

                                cGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACtttt                            >  1:656481/1‑53 (MQ=255)

                                          gatCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:1617911/67‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:502545/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:992747/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:1067090/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:876970/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:3410824/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:3381109/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:3357956/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:3339978/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:2904477/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:2841997/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:2666077/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:2665192/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:2550893/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:1780536/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:1331127/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:1315068/69‑1 (MQ=255)

                                          gTTCGAAGGAGCGATGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAc  <  1:1210917/69‑1 (MQ=255)

TGCAACAAGGGGAAATTTGCGCCTGGATCGCACGAATAAACGGTTCGAAGGAGCGGTGCGTGATTTGTTGCTGAATAAAACTTTTATCCAGCATGACGCGGGTGAAAAGAC  >  minE/1119132‑1119242

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A