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	1,560,414	T→C	23.4%	L141L (TTG→CTG)	evgS →	hybrid sensory histidine kinase in two‑component regulatory system with EvgA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,560,414	0	T	C	23.4%	108.6 / 27.6	85	L141L (TTG→CTG)	evgS	hybrid sensory histidine kinase in two‑component regulatory system with EvgA
Reads supporting (aligned to +/- strand): ref base T (35/30); new base C (6/14); total (41/44)
Fisher's exact test for biased strand distribution p-value = 7.65e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

GATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTC  >  minE/1560348‑1560475

gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCAtt                                                              >  1:1066472/1‑68 (MQ=255)

gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                                             <  1:692491/69‑1 (MQ=255)

gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                                             <  1:786171/69‑1 (MQ=255)

gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                                             <  1:3428047/69‑1 (MQ=255)

gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                                             <  1:2856705/69‑1 (MQ=255)

gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                                             <  1:3232335/69‑1 (MQ=255)

 atatAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                                             <  1:2436847/68‑1 (MQ=255)

  tataGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGAt                                                           <  1:2963419/69‑1 (MQ=255)

  tataGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGAt                                                           <  1:33207/69‑1 (MQ=255)

  tataGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGAt                                                           <  1:2685064/69‑1 (MQ=255)

  tataGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGAt                                                           <  1:541466/69‑1 (MQ=255)

  tataGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGAt                                                           <  1:1707980/69‑1 (MQ=255)

      gtgtTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAAtt                                                       >  1:2898276/1‑69 (MQ=255)

         ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                                    >  1:2472257/1‑69 (MQ=255)

         ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                                    >  1:2271895/1‑69 (MQ=255)

         ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                                    >  1:1715403/1‑69 (MQ=255)

         ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                                    >  1:3196637/1‑69 (MQ=255)

         ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                                    >  1:1600036/1‑69 (MQ=255)

         ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                                    >  1:777748/1‑69 (MQ=255)

         ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                                    >  1:1229893/1‑69 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATTACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:1451483/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTTATAATTACCTTTCCgg                                             <  1:1362709/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:2406511/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:1404590/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:812807/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:2893105/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:2014876/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:3284385/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:527599/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:1895882/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:776585/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:1084148/69‑1 (MQ=255)

                aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:1690143/69‑1 (MQ=255)

                aTTTAGTTCCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                                             <  1:623250/69‑1 (MQ=255)

                        aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCtt                                                  >  1:1410282/1‑56 (MQ=255)

                        aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                                     >  1:1415699/1‑69 (MQ=255)

                        aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                                     >  1:1560251/1‑69 (MQ=255)

                        aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                                     >  1:3113352/1‑69 (MQ=255)

                        aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                                     >  1:2573017/1‑69 (MQ=255)

                        aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                                     >  1:3036438/1‑69 (MQ=255)

                        aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                                     >  1:1197372/1‑69 (MQ=255)

                        aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                                     >  1:195247/1‑69 (MQ=255)

                        aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                                     >  1:2943834/1‑69 (MQ=255)

                           tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                                  >  1:2464606/1‑69 (MQ=255)

                           tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                                  >  1:846277/1‑69 (MQ=255)

                           tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                                  >  1:3079193/1‑69 (MQ=255)

                           tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                                  >  1:3059634/1‑69 (MQ=255)

                           tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                                  >  1:382197/1‑69 (MQ=255)

                           tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                                  >  1:2724846/1‑69 (MQ=255)

                           tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                                  >  1:2308821/1‑69 (MQ=255)

                           tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                                  >  1:760449/1‑69 (MQ=255)

                              ccgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacca                                 <  1:2117696/67‑1 (MQ=255)

                              ccgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacca                                 <  1:3139262/67‑1 (MQ=255)

                               cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                                        >  1:384140/1‑43 (MQ=19)

                               cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                                        >  1:358164/1‑43 (MQ=19)

                               cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                                        >  1:405501/1‑43 (MQ=19)

                               cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                                        >  1:1071745/1‑43 (MQ=19)

                               cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                                        >  1:3091974/1‑43 (MQ=19)

                               cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                                        >  1:276565/1‑43 (MQ=19)

                               cgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacca                                 <  1:449320/66‑1 (MQ=255)

                                   tctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTc                           >  1:1551237/1‑68 (MQ=255)

                                   tctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTc                           >  1:1919997/1‑68 (MQ=255)

                                   tctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTc                           >  1:143559/1‑68 (MQ=255)

                                   tctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTc                           >  1:1243945/1‑68 (MQ=255)

                                          aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc                    <  1:3177761/68‑1 (MQ=255)

                                          aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc                    <  1:1610961/68‑1 (MQ=255)

                                          aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc                    <  1:1417385/68‑1 (MQ=255)

                                          aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc                    <  1:2015156/68‑1 (MQ=255)

                                          aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc                    <  1:3193163/68‑1 (MQ=255)

                                          aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc                    <  1:2483642/68‑1 (MQ=255)

                                          aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc                    <  1:3161870/68‑1 (MQ=255)

                                          aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc                    <  1:3170854/68‑1 (MQ=255)

                                                   gctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc                    <  1:92757/59‑1 (MQ=255)

                                                   gctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCg          >  1:823025/1‑69 (MQ=255)

                                                   gctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCg          >  1:939730/1‑69 (MQ=255)

                                                   gctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCg          >  1:567434/1‑69 (MQ=255)

                                                   gctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCg          <  1:552823/69‑1 (MQ=255)

                                                   gctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCg          >  1:521051/1‑69 (MQ=255)

                                                   gctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCg          <  1:469417/69‑1 (MQ=255)

                                                   gctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCg          >  1:2197171/1‑69 (MQ=255)

                                                      gcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCt        <  1:1927321/68‑1 (MQ=255)

                                                          ccaaaccaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCt   <  1:1864890/69‑1 (MQ=255)

                                                          ccaaaccaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCt   <  1:1652477/69‑1 (MQ=255)

                                                           caaaccaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc                    <  1:193095/51‑1 (MQ=255)

                                                           caaaccaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTc  >  1:1180384/1‑69 (MQ=255)

                                                            ataccaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCt   <  1:526939/65‑1 (MQ=255)

GATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTC  >  minE/1560348‑1560475

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