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	413,265	C→T	27.9%	K306K (AAG→AAA)	lnt ←	apolipoprotein N‑acyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	413,265	0	C	T	27.9%	60.7 / 20.5	57	K306K (AAG→AAA)	lnt	apolipoprotein N‑acyltransferase
Reads supporting (aligned to +/- strand): ref base C (21/20); new base T (14/2); total (35/22)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCTTTACCCAGCGTGATGATGGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCTTTATCACGCAACTCACCGTC  >  minE/413217‑413330

aCCTTTACCCAGCGTGATGATGGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGAc                                               <  1:556577/69‑1 (MQ=255)

aCCTTTACCCAGCGTGATGATGGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGAc                                               <  1:3283049/69‑1 (MQ=255)

aCCTTTACCCAGCGTGATGATGGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGAc                                               <  1:1245425/69‑1 (MQ=255)

aCCTTTACCCAGCGTGATGATGGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGAc                                               <  1:2872504/69‑1 (MQ=255)

aCCTTTACCCAGCGTGATGATGGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGAc                                               <  1:2467426/69‑1 (MQ=255)

               gatgatGGTGTTGTAGGTATCGTAGCGGGTCTGTTTATTGAGACGCGCGTCGACAATCCCGGtg                                     <  1:3311161/64‑2 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTga                                                            >  1:2729285/1‑40 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCTACAATCCCGGTTACCa                                 >  1:296176/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:75985/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:314781/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:2876556/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:2848549/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:2758282/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:3353775/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:2308800/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:344076/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:1227453/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:9259/1‑67 (MQ=255)

                atgatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCa                                 >  1:1339762/1‑67 (MQ=255)

                  gatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCg                              <  1:1871507/68‑1 (MQ=255)

                  gatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCg                              <  1:2570638/68‑1 (MQ=255)

                  gatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCg                              <  1:1328119/68‑1 (MQ=255)

                  gatgGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCg                              <  1:1450682/68‑1 (MQ=255)

                        gttgtAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGa                             <  1:1614600/63‑1 (MQ=255)

                         ttgtAGGTATCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGtg                                     <  1:92906/54‑2 (MQ=39)

                           gtAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCttt                    <  1:2600640/69‑1 (MQ=255)

                           gtAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCttt                    <  1:2611343/69‑1 (MQ=255)

                           gtAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCttt                    <  1:1838563/69‑1 (MQ=255)

                           gtAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCtt                     <  1:1040759/68‑1 (MQ=255)

                           gtAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCtt                     <  1:1214735/68‑1 (MQ=255)

                           gtAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCtt                     <  1:1281658/68‑1 (MQ=255)

                           gtAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCtt                     <  1:1461540/68‑1 (MQ=255)

                           gtAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCtt                     <  1:1745685/68‑1 (MQ=255)

                              ggTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTa                                    >  1:1992657/1‑50 (MQ=255)

                              ggTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCTTTAt                  >  1:822597/1‑68 (MQ=255)

                              ggTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCTTTATc                 >  1:1714689/1‑69 (MQ=255)

                              ggTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCTTTATc                 >  1:2193174/1‑69 (MQ=255)

                              ggTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCACgg                                       >  1:316170/1‑47 (MQ=255)

                               gTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCTTTATCa                >  1:692732/1‑69 (MQ=255)

                                tATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCTTTATCa                >  1:2505720/1‑68 (MQ=255)

                                tATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCTTTATCa                >  1:3129310/1‑68 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:2742767/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:849962/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:707423/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:921579/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:952172/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:431113/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:3310778/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:2757736/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:1951327/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:1309657/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:1158239/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcgc               >  1:1109232/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGGTGACCAGCGAGCTACCTTTATcg                >  1:1601959/1‑66 (MQ=255)

                                 aTCGTAGCGGTTCTGTTTATTGAGACGCGCGTCGACAATCCCGG‑‑ACCAGCGAGCTACCTTTATCGCGCa            >  1:748042/1‑69 (MQ=255)

                                 aTCGTAGCGGTTCTGCTTATTGAGACGCGCGTGGACAATCCCGGTTACCAGCGAGCTACCtt                     <  1:377101/62‑1 (MQ=255)

                                             cTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCTTTATCACGCAACTCACCGTc  <  1:363713/69‑1 (MQ=255)

ACCTTTACCCAGCGTGATGATGGTGTTGTAGGTATCGTAGCGGTTCTGCTTATTGAGACGCGCGTCGACAATCCCGGTTACCAGCGAGCTACCTTTATCACGCAACTCACCGTC  >  minE/413217‑413330

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A