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 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,891,768	G→A	A52T (GCA→ACA)	mdtL →	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,891,768	0	G	A	97.7%	162.8 / NA	43	A52T (GCA→ACA)	mdtL	multidrug efflux system protein
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (19/23); minor base C (1/0); total (20/23)
Fisher's exact test for biased strand distribution p-value = 4.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTATTTCTTGCAGGCCGATTTCTAC  >  NC_000913/3891622‑3891915

gCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGc                                                                                                                                                 >  1:477157/1‑151 (MQ=255)

 cTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCt                                                                                                                                                >  2:21017/1‑151 (MQ=255)

     ttGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCg                                                                                                                                             <  1:629106/150‑1 (MQ=255)

          ttGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGtt                                                                                                                                        >  1:541441/1‑150 (MQ=255)

           tGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTAt                                                                                                                                      >  1:81281/1‑151 (MQ=255)

              aGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATTGACCTCTTTGGTTTACCGCGCACCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTAttt                                                                                                                                    <  1:442089/150‑1 (MQ=255)

                ttttGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGcc                                                                                                                                 >  1:180876/1‑151 (MQ=255)

                    gCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGt                                                                                                                              >  1:161451/1‑150 (MQ=255)

                       cTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGCCAGCTGCGATGTTATTTGCCGGTaa                                                                                                                            >  2:181557/1‑149 (MQ=255)

                             ttACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCg                                                                                                                    >  2:141526/1‑151 (MQ=255)

                                  ttATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATc                                                                                                                 <  1:385420/149‑1 (MQ=255)

                                   tATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGt                                                                                                               <  1:22961/150‑1 (MQ=255)

                                      cccGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTc                                                                                                             >  1:551033/1‑149 (MQ=255)

                                           cgGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAggg                                                                                                         >  1:141704/1‑148 (MQ=255)

                                            gggATTGATATGTGCCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGgaga                                                                                                      <  1:219470/150‑1 (MQ=255)

                                             ggATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGaaa                                                                                                    <  1:239934/151‑1 (MQ=255)

                                              gATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGaa                                                                                                     >  1:90486/1‑149 (MQ=255)

                                              gATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGaa                                                                                                     >  1:454572/1‑149 (MQ=255)

                                              gATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAg                                                                                                   <  2:317472/151‑1 (MQ=255)

                                                ttGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGc                                                                                                  <  2:310723/150‑1 (MQ=255)

                                                        tACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCa                                                                                                            >  2:25907/1‑132 (MQ=255)

                                                        tACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCa                                                                                                            <  1:25907/132‑1 (MQ=255)

                                                          ccTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATa                                                                                       <  1:440431/151‑1 (MQ=255)

                                                             cGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATAccc                                                                                    <  2:357200/151‑1 (MQ=255)

                                                             cGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATAccc                                                                                    <  2:83166/151‑1 (MQ=255)

                                                                      aCCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCcggcgcggcg                                                                           <  1:141529/151‑1 (MQ=255)

                                                                              tCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCtatttat                                                                   >  2:246835/1‑151 (MQ=255)

                                                                               cgccgcCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCtatttatt                                                                  <  2:286255/151‑1 (MQ=255)

                                                                                 ccgccgATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTtattat                                                                <  1:160563/151‑1 (MQ=255)

                                                                                       aTCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGGGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTc                                                          >  2:137429/1‑151 (MQ=255)

                                                                                          tcAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCgg                                                        >  2:416847/1‑150 (MQ=255)

                                                                                           cAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGc                                                             <  1:143625/144‑1 (MQ=255)

                                                                                                      aaGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCtattta                                                                    >  1:137285/1‑126 (MQ=255)

                                                                                                      aaGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCtattta                                                                    <  2:137282/126‑1 (MQ=255)

                                                                                                              ttGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGaa                                    >  1:63876/1‑150 (MQ=255)

                                                                                                               tGCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAAc                                  >  2:343392/1‑151 (MQ=255)

                                                                                                                gCATATTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAAc                                  <  1:262195/150‑1 (MQ=255)

                                                                                                                    atTGCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTACCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCa                             <  1:210/151‑1 (MQ=255)

                                                                                                                       gCGTTCTCCGTATATCTGGCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGt                          >  1:120091/1‑151 (MQ=255)

                                                                                                                                        ggCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTATTTCTTGCAGGcc           <  2:176490/149‑1 (MQ=255)

                                                                                                                                         gCGGGGATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTATTTCTTGCAGGCCGAt        <  2:90486/151‑1 (MQ=255)

                                                                                                                                             ggATGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTATTTCTTGCAGGCCGATTTCt    <  2:376452/151‑1 (MQ=255)

                                                                                                                                               aTGACAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTATTTCTTGCAGGCCGATTTCTAc  <  2:443839/151‑1 (MQ=255)

GCTTTTTGATTTGTAGTTTTGCCCTGGTTTTACTTTATCCCGCCGGGATTGATATGTACCTCGTTGGTTTACCGCGCATCGCCGCCGATCTCAATGCCAGCGAAGCGCAGTTGCATATTGCGTTCTCCGTATATCTGGCGGGGATGGCAGCTGCGATGTTATTTGCCGGTAAAGTGGCCGATCGTTCAGGGAGAAAGCCGGTCGCCATACCCGGCGCGGCGCTATTTATTATTGCCTCGGTGTTCTGTTCACTGGCTGAAACCAGCACGTTATTTCTTGCAGGCCGATTTCTAC  >  NC_000913/3891622‑3891915

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A