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
A7 F50 I2 R1	209	44.2	1360995	98.7%	1343302	150.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,339,460	C→T	intergenic (‑40/‑107)	gyrA ← / → ubiG	DNA gyrase (type II topoisomerase), subunit A/bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,339,460	0	C	T	100.0%	183.5 / NA	48	intergenic (‑40/‑107)	gyrA/ubiG	DNA gyrase (type II topoisomerase), subunit A/bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (20/28); total (20/28)

GGCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTCGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCGCCGGTAAACCATAACGTAGACCA  >  NC_000913/2339317‑2339607

ggCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCaaa                                                                                                                                                <  1:73939/149‑1 (MQ=255)

ggCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCa                                                                                                                                                  <  1:463594/147‑1 (MQ=255)

ggCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAAt                                                                                                                                               <  2:574706/150‑1 (MQ=255)

    gcgcACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATaa                                                                                                                                          <  2:455406/151‑1 (MQ=255)

    gcgcACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATaa                                                                                                                                          <  2:43420/151‑1 (MQ=255)

           gCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGGTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGcc                                                                                                                                   >  2:305632/1‑151 (MQ=255)

                    gACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGttt                                                                                                                          <  2:436622/151‑1 (MQ=255)

                       cGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAg                                                                                                                       <  2:549170/151‑1 (MQ=255)

                       cGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAg                                                                                                                       <  1:499823/151‑1 (MQ=255)

                              gCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTGCTGTATCCCGGATTCAAAGGTTGCAAATTATAACGCAGCCGCGCAGTTTGAGGTAAAcc                                                                                                                <  2:585425/151‑1 (MQ=255)

                                aTAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCta                                                                                                              <  1:281068/151‑1 (MQ=255)

                                  aaTCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCtata                                                                                                            <  2:541239/151‑1 (MQ=255)

                                    tCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACg                                                                                                          >  1:121133/1‑151 (MQ=255)

                                                   ttcagctcttcCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATcc                                                                                            >  1:63300/1‑150 (MQ=255)

                                                    tcagctcttcCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCa                                                                                           <  2:283897/150‑1 (MQ=255)

                                                     cagctcttcCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTAGCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCaa                                                                                          <  2:576853/150‑1 (MQ=255)

                                                                  aTGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTc                                                                            <  1:314364/151‑1 (MQ=255)

                                                                    gTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCg                                                                           <  2:55478/150‑1 (MQ=255)

                                                                       gACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTg                                                                       >  2:23930/1‑151 (MQ=255)

                                                                       gACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCGCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTg                                                                       <  2:189475/151‑1 (MQ=255)

                                                                         ccGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTc                                                                     <  1:465785/151‑1 (MQ=255)

                                                                           ggTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCtt                                                                   <  2:22220/151‑1 (MQ=255)

                                                                                      tctcGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACgg                                                        >  1:22218/1‑151 (MQ=255)

                                                                                       ctcGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTAc                                                          <  2:433098/148‑1 (MQ=255)

                                                                                       ctcGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTAc                                                          <  2:254296/148‑1 (MQ=255)

                                                                                       ctcGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACg                                                         <  2:416383/149‑1 (MQ=255)

                                                                                         cGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGa                                                       <  2:331672/149‑1 (MQ=255)

                                                                                         cGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGt                                                     >  1:270977/1‑151 (MQ=255)

                                                                                              ggTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGa                                                  >  2:272676/1‑149 (MQ=255)

                                                                                                tCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTg                                              >  2:640739/1‑151 (MQ=255)

                                                                                                        cTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCaatga                                       >  1:638488/1‑150 (MQ=255)

                                                                                                          aaCCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCtat                                                                                                             <  1:72486/78‑1 (MQ=255)

                                                                                                          aaCCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCtat                                                                                                             >  2:72483/1‑78 (MQ=255)

                                                                                                          aaCCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCaatgaatg                                    >  1:209207/1‑151 (MQ=255)

                                                                                                             cGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCg                                 <  2:343593/151‑1 (MQ=255)

                                                                                                             cGCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCg                                 >  2:370774/1‑151 (MQ=255)

                                                                                                              gCTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCg                                 >  2:675311/1‑150 (MQ=255)

                                                                                                               cTATCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGa                                >  1:135401/1‑150 (MQ=255)

                                                                                                                 aTCCCTCTACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGaaa                              <  2:303549/150‑1 (MQ=255)

                                                                                                                     ctctACTGTATCCCGGATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCg                         >  1:519859/1‑151 (MQ=255)

                                                                                                                                    gATTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCGCCGGTAAACCATAAc          <  1:155206/151‑1 (MQ=255)

                                                                                                                                     aTTCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCGCCGGTAAACCATAACg         >  2:335110/1‑151 (MQ=255)

                                                                                                                                      ttCAAAGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCGCCGGTAAACCATAACGt        >  1:263786/1‑151 (MQ=255)

                                                                                                                                         aaaGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCGCCGGTAAACCATAACGt        >  1:265631/1‑148 (MQ=255)

                                                                                                                                         aaaGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCGCCGGTAAACCATAACGt        >  2:93229/1‑148 (MQ=255)

                                                                                                                                         aaaGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCGCCGGTAAACCATAACGTAGa     <  2:64674/151‑1 (MQ=255)

                                                                                                                                          aaGGTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCGCCGGTAAACCATAACGTAGAc    >  1:513209/1‑151 (MQ=255)

                                                                                                                                            ggTTGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCGCCGGTAAACCATAACGTAGACCa  <  2:576069/151‑1 (MQ=255)

GGCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTCGCAAATTATAACACAGCCGCGCAGTTTGAGGTAAACCTATACGCTTTATTCACATCCAATGCCTGATATACTCGTTTGTCTTGCCAATTACGGAGTAGAAGTGCCAATGAATGCCGAAAAATCGCCGGTAAACCATAACGTAGACCA  >  NC_000913/2339317‑2339607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `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