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	1,096,275	A→G	57.0%	S34S (AGT→AGC)	ydiJ ←	predicted FAD‑linked oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,096,275	0	A	G	57.0%	19.4 / 47.0	65	S34S (AGT→AGC)	ydiJ	predicted FAD‑linked oxidoreductase
Reads supporting (aligned to +/- strand): ref base A (17/11); new base G (7/30); total (24/41)
Fisher's exact test for biased strand distribution p-value = 7.57e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATACCACCGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAAC  >  minE/1096208‑1096343

aTACCACCGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATaa                                                                      >  1:208116/1‑68 (MQ=255)

aTACCACCGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAAc                                                                     >  1:1105132/1‑69 (MQ=255)

aTACCACCGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAAc                                                                     >  1:2071269/1‑69 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:3142556/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:1741706/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:1781514/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:187928/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:2304875/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:2571207/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:2590069/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:2834420/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:2910780/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:3138654/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:2389685/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:517632/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:549070/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:715412/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:720416/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:744616/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:831556/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:959935/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:985887/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:994920/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:1346182/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:1352596/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:1402783/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:1255700/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:1173555/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:1347198/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:1158750/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:1587471/69‑1 (MQ=255)

  accaccGCATCGGGGAGAAGTTCGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:2458400/69‑1 (MQ=255)

   ccaccGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCtt                                                                   <  1:2404678/68‑1 (MQ=255)

                             aTACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCTTGTTGCCGTATCGCCGGTAAAACCctgt                                        >  1:2059181/1‑69 (MQ=255)

                             aTACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCTTGTTGCCGTATCGCCGGTAAAACCctgt                                        >  1:1065922/1‑69 (MQ=255)

                             aTACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCTTGTTGCCGTATCGCCGGTAAAACCctgt                                        >  1:3337701/1‑69 (MQ=255)

                             aTACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCTTGTTGCCGTATCGCCGGTAAAACCctgt                                        >  1:3434709/1‑69 (MQ=255)

                             aTACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCTTGTTGCCGTATCGCCGGTAAAACCctgt                                        >  1:531372/1‑69 (MQ=255)

                             aTACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCTTGTTGCCGTATCGCCGGTAAAACCctgt                                        >  1:456009/1‑69 (MQ=255)

                             aTACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAGCTTGTTGCCGTATCGCCGGTAAAACCctg                                         >  1:1813723/1‑68 (MQ=255)

                               aCTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACtt                                                                   >  1:1295140/1‑40 (MQ=255)

                               aCTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACtt                                                                   >  1:2853645/1‑40 (MQ=255)

                               aCTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACtt                                                                   >  1:490015/1‑40 (MQ=255)

                               aCTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACtt                                                                   >  1:405684/1‑40 (MQ=255)

                               aCTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACtt                                                                   >  1:2812793/1‑40 (MQ=255)

                               aCTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACtt                                                                   >  1:1393919/1‑40 (MQ=255)

                               aCTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACtt                                                                   >  1:683877/1‑40 (MQ=255)

                               aCTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACtt                                                                   >  1:209998/1‑40 (MQ=255)

                               aCTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACtt                                                                   >  1:1515963/1‑40 (MQ=255)

                               aCTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACtt                                                                   >  1:1604853/1‑40 (MQ=255)

                                                  gTCAGACGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTGTTGCaaaaa                    >  1:1361515/1‑68 (MQ=255)

                                                  gTCAGACGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCaaaaa                    >  1:115895/1‑68 (MQ=255)

                                                  gTCAGACGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCaaaaa                    >  1:1112234/1‑68 (MQ=255)

                                                  gTCAGACGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCaaaa                     >  1:3245038/1‑67 (MQ=255)

                                                  gTCAGACGATCGGCATAACTTGTCGCCGTATAGCCGGTAAAACCTTGTTGCTCCAGctct                            >  1:1045913/1‑60 (MQ=255)

                                                       aCGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAg              <  1:884742/69‑1 (MQ=255)

                                                       aCGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAg              <  1:297080/69‑1 (MQ=255)

                                                       aCGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAg              <  1:2839316/69‑1 (MQ=255)

                                                       aCGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAg              <  1:2835542/69‑1 (MQ=255)

                                                       aCGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAg              <  1:2330567/69‑1 (MQ=255)

                                                       aCGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAg              <  1:3125547/69‑1 (MQ=255)

                                                                aTAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTg     <  1:237719/69‑1 (MQ=255)

                                                                aTAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTg     <  1:163097/69‑1 (MQ=255)

                                                                aTAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTg     <  1:1546017/69‑1 (MQ=255)

                                                                aTAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTg     <  1:2560182/69‑1 (MQ=255)

                                                                aTAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTATTGCAAAAAATTAAGCACCAGTTg     <  1:15674/69‑1 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCTGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  >  1:3153511/1‑69 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTg     >  1:1854245/1‑66 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  >  1:1042358/1‑69 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  >  1:1290757/1‑69 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  <  1:126493/69‑1 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  <  1:640253/69‑1 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  <  1:1444158/69‑1 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  >  1:1965373/1‑69 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  >  1:2819820/1‑69 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  >  1:3215482/1‑69 (MQ=255)

                                                                   aCTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  >  1:1827856/1‑69 (MQ=255)

                                                                   aCTTGTAGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAac  >  1:442313/1‑69 (MQ=255)

ATACCACCGCATCGGGGAGAAGTTGGTAAATACTGTTGTCGGTCGACATTGTCAGACGATCGGCATAACTTGTCGCCGTATCGCCGGTAAAACCTTGTTGCTCCAGCTCTTGCAAAAAATTAAGCACCAGTTGAAC  >  minE/1096208‑1096343

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