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	494,552	T→C	51.7%	A247A (GCA→GCG)	galM ←	galactose‑1‑epimerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	494,552	0	T	C	51.7%	1.4 / 50.5	60	A247A (GCA→GCG)	galM	galactose‑1‑epimerase
Reads supporting (aligned to +/- strand): ref base T (15/14); new base C (15/16); total (30/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCATCTGCTGACCAGACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCGATGATTTTG  >  minE/494490‑494618

tCATCTGCTGACCAGACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTg                                                               <  1:1669140/68‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:458169/69‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:1184655/69‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:3388712/69‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:1368082/69‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:244714/69‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:2256631/69‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:212554/69‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:2096067/69‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:689550/69‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:1644626/69‑1 (MQ=255)

              gACATGCGCCGCCACTTTCTTGCCATAGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:529126/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:363457/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:553072/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:3115828/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:3006087/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:3144933/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:3200500/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:619086/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:2405334/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:2127158/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:2056327/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:1730390/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:2039200/69‑1 (MQ=255)

                cATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:651099/69‑1 (MQ=255)

                cATGCCCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:1502542/69‑1 (MQ=255)

                 aTGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:559007/68‑1 (MQ=255)

                  tGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCACTTTg                                            >  1:1590445/1‑69 (MQ=255)

                    cgccgcCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCACTTTgcg                                          >  1:2732206/1‑69 (MQ=255)

                       cgccACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:262219/60‑1 (MQ=255)

                                       tCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCAc                                                <  1:2043947/44‑1 (MQ=255)

                                         gCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCACTTTTCGCTGATCGTCGTCGGCAAGaaa                     >  1:3066671/1‑69 (MQ=255)

                                         gCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGaaa                     >  1:1938395/1‑69 (MQ=255)

                                          ccTTTGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACtt                                              <  1:1531070/43‑1 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAacacac                >  1:849732/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:3185526/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:3284929/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:477212/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:1237850/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:2582734/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:104680/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:2893779/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:2758903/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:1634538/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:149438/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:2333578/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:2309062/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:879286/1‑69 (MQ=255)

                                              tGGCCTGTAACAAGAACGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCAc                >  1:801098/1‑69 (MQ=255)

                                                       aCAAGAATGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGaaa                     >  1:3213343/1‑55 (MQ=255)

                                                       aCAAGAATGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCgatga       >  1:1051393/1‑69 (MQ=255)

                                                       aCAAGAATGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCgatga       >  1:2032749/1‑69 (MQ=255)

                                                       aCAAGAATGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCgatga       >  1:1951987/1‑69 (MQ=255)

                                                       aCAAGAATGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCgatga       >  1:1499551/1‑69 (MQ=255)

                                                       aCAAGAATGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAAATCACTGGCgatga       >  1:3134083/1‑69 (MQ=255)

                                                            aaTGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCGATGAtttt   >  1:313088/1‑68 (MQ=255)

                                                            aaTGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCGATGATTTTg  >  1:246354/1‑69 (MQ=255)

                                                            aaTGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCGATGATTTTg  >  1:714127/1‑69 (MQ=255)

                                                            aaTGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCGATGATTTTg  >  1:1833827/1‑69 (MQ=255)

                                                            aaTGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCGATGATTTTg  >  1:1723366/1‑69 (MQ=255)

TCATCTGCTGACCAGACATGCGCCGCCACTTTCTTGCCATCGCCTTTGGCCTGTAACAAGAATGCGTGATCGTAACCTTTCACTTTGCGCTGATCGTCGTCGGCAAGAAACTCACTGGCGATGATTTTG  >  minE/494490‑494618

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