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	1,532,988	A→G	49.1%	T235T (ACT→ACC)	prmB ←	N5‑glutamine methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,532,988	0	A	G	49.1%	‑6.0 / 51.1	57	T235T (ACT→ACC)	prmB	N5‑glutamine methyltransferase
Reads supporting (aligned to +/- strand): ref base A (8/21); new base G (22/6); total (30/27)
Fisher's exact test for biased strand distribution p-value = 1.70e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.37e-01

CCATCATCAGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTCG  >  minE/1532926‑1533042

ccATCATCAGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCa                                                  <  1:1791383/69‑1 (MQ=255)

ccATCATCAGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCa                                                  <  1:1732062/69‑1 (MQ=255)

ccATCATCAGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCa                                                  <  1:536417/69‑1 (MQ=255)

ccATCATCAGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCa                                                  <  1:2479189/69‑1 (MQ=255)

ccATCATCAGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCa                                                  <  1:151940/69‑1 (MQ=255)

ccATCATCAGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCa                                                  <  1:1571598/69‑1 (MQ=255)

 catcatCAGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCa                                                  <  1:2198218/68‑1 (MQ=255)

     atcaGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCa                                                  >  1:13387/1‑64 (MQ=255)

     atcaGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGAt                                               >  1:3062253/1‑67 (MQ=255)

     atcaGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGAt                                               >  1:803578/1‑67 (MQ=255)

     atcaGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGAt                                               >  1:662342/1‑67 (MQ=255)

     atcaGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGAt                                               >  1:1554935/1‑67 (MQ=255)

     atcaGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGAt                                               >  1:2592163/1‑67 (MQ=255)

                   cTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCg                               >  1:1377236/1‑69 (MQ=255)

                    tGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCg                               >  1:81175/1‑68 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:471664/69‑1 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:428468/69‑1 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:2600999/69‑1 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:359206/69‑1 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:3078580/69‑1 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:1863726/69‑1 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:1780471/69‑1 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:1698573/69‑1 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:1347696/69‑1 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:830593/69‑1 (MQ=255)

                                gagaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:1186644/69‑1 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:865044/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:1216770/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:1327621/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:2622736/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:1434617/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:1824874/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:833071/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:629469/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:1713197/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:2158315/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTAt                 >  1:69819/1‑69 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:3392177/68‑1 (MQ=255)

                                 agaATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:918297/68‑1 (MQ=255)

                                            cgTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGTGTTCCGGCTCGTGGCGGTATTCGTTTGGCAg      <  1:2454019/69‑1 (MQ=255)

                                            cgTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAg      <  1:1363975/69‑1 (MQ=255)

                                            cgTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAg      <  1:146431/69‑1 (MQ=255)

                                            cgTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAg      <  1:168046/69‑1 (MQ=255)

                                            cgTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAg      <  1:2079523/69‑1 (MQ=255)

                                            cgTCAGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAg      <  1:1926338/69‑1 (MQ=255)

                                             gTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTa                  <  1:345114/56‑1 (MQ=255)

                                                aGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGtg   >  1:259405/1‑67 (MQ=255)

                                                aGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTc   >  1:2980474/1‑68 (MQ=255)

                                                aGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTCg  >  1:2300387/1‑69 (MQ=255)

                                                aGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTCg  >  1:1673822/1‑69 (MQ=255)

                                                aGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTCg  >  1:1801012/1‑69 (MQ=255)

                                                aGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTCg  >  1:756519/1‑69 (MQ=255)

                                                aGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTCg  >  1:3191484/1‑69 (MQ=255)

                                                aGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTCg  >  1:2585475/1‑69 (MQ=255)

                                                aGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTCg  >  1:2729403/1‑69 (MQ=255)

                                                aGTTTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTCg  >  1:3392044/1‑69 (MQ=255)

                                                aGTCTCAGGCCGTCGGTGCCAGATGCCAGACCGAGTTCCGGCTCGTGTCGGTATTCGTTTGGCAGGTCg  >  1:244740/1‑69 (MQ=255)

CCATCATCAGCAAGGTAATCTGCCGCGTTACCGAGAATGCGACGCGTCAGTTTCAGGCCGTCAGTGCCAGATGCCAGGCCCAGTTCCGGCTCGTGGCGGTATTCGTTTGGCAGGTCG  >  minE/1532926‑1533042

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