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	2,209,246	C→T	58.2%	L765L (TTG→TTA)	yhdP ←	conserved membrane protein, predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,209,246	0	C	T	58.2%	19.4 / 48.6	67	L765L (TTG→TTA)	yhdP	conserved membrane protein, predicted transporter
Reads supporting (aligned to +/- strand): ref base C (18/10); new base T (18/21); total (36/31)
Fisher's exact test for biased strand distribution p-value = 2.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCACCAGCATGATAAGGCAGATCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGTTTAC  >  minE/2209187‑2209314

gCACCAGCATTATAAGGCAGATCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTCAATGCTTCg                                                             >  1:488045/1‑69 (MQ=255)

gCACCAGCATGATAAGGCAGATCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTCAATGCTTCg                                                             >  1:1600220/1‑69 (MQ=255)

gCACCAGCATGATAAGGCAGATCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTCAATGCTTCg                                                             >  1:443049/1‑69 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGGCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:375781/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGct                                             <  1:1084653/69‑2 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:3078578/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:2979703/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:28359/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:2802799/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:3270562/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:2598161/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:2542226/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:524175/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:534064/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:2311846/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:2447542/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:2008535/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:1892009/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:1666195/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:1075382/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:1088711/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:1178068/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:1599798/69‑1 (MQ=255)

                gCAGCTCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCa                                             <  1:1321568/69‑1 (MQ=255)

                     tCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTCAATGCTTCGtt                                                           >  1:2807689/1‑50 (MQ=255)

                     tCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAAc                                         >  1:1513742/1‑68 (MQ=255)

                     tCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACg                                        >  1:3236865/1‑69 (MQ=255)

                     tCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACg                                        >  1:2888967/1‑69 (MQ=255)

                           cccACTTTACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACGcc                                      <  1:2335615/65‑1 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGGAGGCAGAAAGCCGGttt                                 >  1:100417/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:1458513/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:880731/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:356371/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:1082859/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:2042779/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:3125426/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:868701/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:458121/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:2971713/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:2878325/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:1191090/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:2401979/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:2804473/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:1284335/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:2750930/1‑69 (MQ=255)

                            ccACTTTACCATCCCACGCCACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:2493100/1‑69 (MQ=255)

                            ccACTTTACCATCACACGCAACGCTGCCACTTAATGCTTCGTTCACCGCTGCAGGCAGAAAGCCGGttt                                 >  1:3289621/1‑69 (MQ=255)

                                  tACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCg                           >  1:2856207/1‑69 (MQ=255)

                                  tACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCg                           >  1:2176793/1‑69 (MQ=255)

                                  tACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCg                           >  1:1317547/1‑69 (MQ=255)

                                  tACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCg                           >  1:265306/1‑69 (MQ=255)

                                  tACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCg                           >  1:135517/1‑69 (MQ=255)

                                              ccacgcTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTAc               <  1:2978804/69‑1 (MQ=255)

                                                   cTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAg                                            >  1:776439/1‑35 (MQ=255)

                                                   cTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAg                                            >  1:1027064/1‑35 (MQ=255)

                                                   cTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAg                                            >  1:957393/1‑35 (MQ=255)

                                                   cTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAg                                            >  1:2113925/1‑35 (MQ=255)

                                                   cTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAg                                            >  1:1885463/1‑35 (MQ=255)

                                                   cTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAg                                            >  1:1664497/1‑35 (MQ=255)

                                                        aCTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGtt     <  1:354775/69‑1 (MQ=255)

                                                        aCTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGtt     <  1:3021856/69‑1 (MQ=255)

                                                        aCTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGtt     <  1:477970/69‑1 (MQ=255)

                                                        aCTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGtt     <  1:2502317/69‑1 (MQ=255)

                                                        aCTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGtt     <  1:2492850/69‑1 (MQ=255)

                                                        aCTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGtt     <  1:71090/69‑1 (MQ=255)

                                                        aCTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGtt     <  1:2267036/69‑1 (MQ=255)

                                                        aCTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGtt     <  1:974101/69‑1 (MQ=255)

                                                           cAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGTTTAc  >  1:2678636/1‑69 (MQ=255)

GCACCAGCATGATAAGGCAGATCAATGCCCACTTTACCATCCCACGCCACGCTGCCACTCAATGCTTCGTTCACCGCTTCAGGCAGAACGCCGGTTTTCGCCGGTTGCCAGTTACCGTTGAGGTTTAC  >  minE/2209187‑2209314

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