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	1,483,604	T→C	38.8%	L178L (TTA→CTA)	glpC →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), small subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,483,604	0	T	C	38.8%	22.9 / 34.0	54	L178L (TTA→CTA)	glpC	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), small subunit
Reads supporting (aligned to +/- strand): ref base T (19/14); new base C (4/17); total (23/31)
Fisher's exact test for biased strand distribution p-value = 1.02e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.86e-01

TAAAGACCAGGTCGCTTTCTTTCACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCAAAGAAA  >  minE/1483549‑1483670

taAAGACCAGGTCGCTTTCTTTCACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGAttt                                                       >  1:196454/1‑69 (MQ=255)

taAAGACCAGGTCGCTTTCTTTAACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGAttt                                                       >  1:2021230/1‑69 (MQ=255)

            cGCTTTCTTTCACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGc                                            >  1:1179022/1‑68 (MQ=255)

            cGCTTTCCTTCACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGc                                            >  1:1371909/1‑68 (MQ=255)

               tttctttcACGGCTGCTTCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGc                                            >  1:2057252/1‑65 (MQ=255)

               tttctttcACGGCTGCTTCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGc                                            >  1:60446/1‑65 (MQ=255)

               tttctttcACGGCTGCTTCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGc                                            >  1:1502421/1‑65 (MQ=255)

               tttctttcACGGCTGCTTCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGc                                            >  1:504165/1‑65 (MQ=255)

                   tttcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGc                                     <  1:991563/68‑1 (MQ=255)

                   tttcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGc                                     <  1:2075198/68‑1 (MQ=255)

                   tttcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGc                                     <  1:1786442/68‑1 (MQ=255)

                   tttcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGc                                     <  1:1774358/68‑1 (MQ=255)

                   tttcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGc                                     <  1:3308311/68‑1 (MQ=255)

                   tttcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGc                                     <  1:58547/68‑1 (MQ=255)

                   tttcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGc                                     <  1:1337307/68‑1 (MQ=255)

                     tcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATttaatta                                                  >  1:3241588/1‑53 (MQ=255)

                     tcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATttaatta                                                  >  1:132604/1‑53 (MQ=255)

                     tcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATttaatta                                                  >  1:313229/1‑53 (MQ=255)

                     tcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATttaatta                                                  >  1:667898/1‑53 (MQ=255)

                     tcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATttaatta                                                  >  1:671928/1‑53 (MQ=255)

                     tcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATttaatta                                                  >  1:840736/1‑53 (MQ=255)

                     tcACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATttaatta                                                  >  1:2588336/1‑53 (MQ=255)

                     tcACGGCTGCTTCGTTAACTACAACCATACGCAGTTAGGTAAAGATttaatta                                                  >  1:305104/1‑53 (MQ=255)

                                tCGTTAACTACAACCATCCGTAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:254163/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGTGTACCGgtg                       <  1:2879903/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:2388475/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:2523491/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:1897036/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:3130724/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:1854527/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:934841/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:3152756/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:92955/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:1203285/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:1605355/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:716895/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:1282679/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:407469/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:616212/69‑1 (MQ=255)

                                tCGTTAACTACAACCATCCGCAGCTAGGCAAAGATTTAATTAAAGTGCTCAACGCGATGGGTACCGgtg                       <  1:583793/69‑1 (MQ=255)

                                          cAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCa                                    >  1:1116641/1‑46 (MQ=255)

                                          cAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTg               >  1:1315227/1‑67 (MQ=255)

                                          cAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTg               >  1:3372386/1‑67 (MQ=255)

                                          cAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTg               >  1:1236534/1‑67 (MQ=255)

                                          cAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTg               >  1:317459/1‑67 (MQ=255)

                                                  cGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCaaa      >  1:61656/1‑68 (MQ=255)

                                                  cGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCaaa      >  1:3150327/1‑68 (MQ=255)

                                                     aGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCAAAGaaa  <  1:1394232/69‑1 (MQ=255)

                                                     aGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCAAAGaaa  <  1:1533599/69‑1 (MQ=255)

                                                     aGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCAAAGaaa  <  1:621828/69‑1 (MQ=255)

                                                     aGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCAAAGaaa  <  1:3335070/69‑1 (MQ=255)

                                                     aGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCAAAGaaa  <  1:72677/69‑1 (MQ=255)

                                                     aGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCAAAGaaa  <  1:1679626/69‑1 (MQ=255)

                                                     aGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCAAAGaaa  <  1:1010980/69‑1 (MQ=255)

TAAAGACCAGGTCGCTTTCTTTCACGGCTGCTTCGTTAACTACAACCATCCGCAGTTAGGTAAAGATTTAATTAAAGTGCTCAACGCAATGGGTACCGGTGTACAACTGCTCAGCAAAGAAA  >  minE/1483549‑1483670

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