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
A1 F28 I2 R1	330	0.0	2544031	91.9%	2337964	62.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	1,771,192	(G)_7→6	coding (405/1113 nt)	ydiK →	predicted inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,771,186	0	G	.	80.0%	102.8 / 36.8	45	coding (399/1113 nt)	ydiK	predicted inner membrane protein
Reads supporting (aligned to +/- strand): ref base G (7/2); new base . (0/36); total (7/38)
Fisher's exact test for biased strand distribution p-value = 7.93e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

AATACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATGGGGGGGACGGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACC  >  W3110S.gb/1771127‑1771234

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:2332427/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:1713420/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:1744551/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:430101/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:553879/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:1567522/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:388348/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:315803/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:2230266/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:690163/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:2264077/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:2515640/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:2355478/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:1308554/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:840708/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:1200889/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATgggggg                                             >  1:954639/1‑65 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATggggg                                              >  1:802564/1‑64 (MQ=255)

aaTACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATg                                                  >  1:1113462/1‑60 (MQ=255)

                  ggCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATGGGGGGGACgg                                        <  1:1109140/52‑1 (MQ=255)

                  ggCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATGGGGGGGACgg                                        <  1:1517982/52‑1 (MQ=255)

                      cgAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATGGGGGGGACGGCGATCATGGCGAAAGt                        >  1:1310848/1‑64 (MQ=255)

                      cgAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATGGGGGGGACGGCGATCATGGCGAAAGTc                       >  1:1825594/1‑65 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:528743/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:472120/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:461470/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:456039/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:442885/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:553875/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:319695/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:555690/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:680014/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:829069/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:831639/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:2388501/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:985787/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:2276584/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1253310/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1318948/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1341994/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1352901/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1362746/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:138989/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:141884/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1616389/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1641930/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1796314/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1814098/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1872772/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1981632/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:2313742/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:2269558/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:2195940/65‑1 (MQ=255)

                         aGCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:2027981/65‑1 (MQ=255)

                          gCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:17607/64‑1 (MQ=255)

                          gCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1109044/64‑1 (MQ=255)

                          gCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:1136162/64‑1 (MQ=255)

                          gCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:808366/64‑1 (MQ=255)

                          gCTGTATGCAGGCTGGCACAACTTGCTGGATAT‑GGGGGGACGGCGATCATGGCGAAAGTCCGcc                   <  1:640994/64‑1 (MQ=255)

                                           actaCTTGCTGGATATGGGGGGGACGGCGATCATGGCGAAAGTCCGCCCTTATATTGGcaccacc  >  1:327119/4‑65 (MQ=255)

                                           acaACTTGCTGGATATGGGGGGGACGGCGATCATGGCGAAAGTCCGCCCTTATATTGGcaccacc  >  1:782018/1‑65 (MQ=255)

                                           acaACTTGCTGGATATGGGGGGGACGGCGATCATGGCGAAAGTCCGCCCTTATATTGGcaccacc  >  1:329499/1‑65 (MQ=255)

                                           acaACTTGCTGGATATGGGGGGGACGGCGATCATGGCGAAAGTCCGCCCTTATATTGGcaccacc  >  1:2023252/1‑65 (MQ=255)

                                           acaACTTGCTGGATATGGGGGGGACGGCGATCATGGCGAAAGTCCGCCCTTATATTGGcaccacc  >  1:1567775/1‑65 (MQ=255)

AATACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTGCTGGATATGGGGGGGACGGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACC  >  W3110S.gb/1771127‑1771234

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