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
A12 F28 I1 R1	227	52.0	1764248	99.3%	1751898	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,882,057	A→G	E49G (GAG→GGG)	dmlA →	D‑malate/3‑isopropylmalate dehydrogenase (decarboxylating)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,882,057	0	A	G	100.0%	115.2 / NA	33	E49G (GAG→GGG)	dmlA	D‑malate/3‑isopropylmalate dehydrogenase (decarboxylating)
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/16); total (17/16)

TGCGTATTGCTGCGATCCCGGGAGACGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGAGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGTTCCGGACCATATTTCGTTG  >  NC_000913/1881925‑1882178

tGCGTATTGCTGCGATCCCGGGAGACGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTAc                                                                                                                    >  2:819066/1‑140 (MQ=255)

      ttGCTGCGATCCCGGGAGACGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCAt                                                                                                              <  1:12678/140‑1 (MQ=255)

        gctgcGATCCCGGGAGACGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCa                                                                                                            <  1:48970/140‑1 (MQ=255)

           gcGATCCCGGGAGACGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACgg                                                                                                         <  1:805428/140‑1 (MQ=255)

                    ggAGACGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAatgat                                                                                                >  1:834789/1‑140 (MQ=255)

                     gagaCGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAatgatg                                                                                               <  1:108676/140‑1 (MQ=255)

                        aCGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCg                                                                                            >  2:117570/1‑140 (MQ=255)

                        aCGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCg                                                                                            <  1:689247/140‑1 (MQ=255)

                         cGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCgg                                                                                           >  2:332334/1‑140 (MQ=255)

                            gATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGgacg                                                                                        >  2:778588/1‑140 (MQ=255)

                                                     gggATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGttt                                                               <  1:647829/140‑1 (MQ=255)

                                                         ttCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGAc                                                           <  1:239107/140‑1 (MQ=255)

                                                         ttCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGAc                                                           >  1:477300/1‑140 (MQ=255)

                                                          tCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACg                                                          <  2:88523/140‑1 (MQ=255)

                                                          tCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACg                                                          >  1:714430/1‑140 (MQ=255)

                                                            gcgTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGcc                                                        <  1:332334/140‑1 (MQ=255)

                                                              gtgtTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCAt                                                      <  1:819066/140‑1 (MQ=255)

                                                                           ccGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGcc                                         >  2:47725/1‑140 (MQ=255)

                                                                           ccGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGcc                                         >  2:72243/1‑140 (MQ=255)

                                                                           ccGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGcc                                         >  1:457476/1‑140 (MQ=255)

                                                                            cGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCg                                        >  1:394285/1‑140 (MQ=255)

                                                                                 aGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGc                                   >  2:763234/1‑140 (MQ=255)

                                                                                      tGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGcc                              <  1:424583/140‑1 (MQ=255)

                                                                                             tCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATAcc                       >  2:755429/1‑140 (MQ=255)

                                                                                                ccTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGtt                    >  1:8530/1‑140 (MQ=255)

                                                                                                ccTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGtt                    >  1:764206/1‑140 (MQ=255)

                                                                                                ccTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGtt                    <  1:763234/140‑1 (MQ=255)

                                                                                                     aGTTTTGAGCAAATGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGTTCCGGa               <  1:47725/140‑1 (MQ=255)

                                                                                                                  tGGAGTGGGCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGTTCCGGACCATATTTCGTtg  <  2:764206/140‑1 (MQ=255)

                                                                                                                         ggCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGTTCCGGACCATAtt        >  1:649179/1‑127 (MQ=255)

                                                                                                                         ggCGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGTTCCGGACCATAtt        <  2:649179/127‑1 (MQ=255)

                                                                                                                           cGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGTTCCGGACCATAtt        >  1:621770/1‑125 (MQ=255)

                                                                                                                           cGAGCTGCGGGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGTTCCGGACCATAtt        <  2:621770/125‑1 (MQ=255)

TGCGTATTGCTGCGATCCCGGGAGACGGGATTGGCAAAGAAGTCCTTCCTGAAGGGATTCGCGTGTTACAGGCTGCCGCTGAGCGCTGGGGCTTCGCCTTGAGTTTTGAGCAAATGGAGTGGGCGAGCTGCGAGTATTACAGCCATCACGGTAAAATGATGCCGGACGACTGGCATGAGCAACTTAGCCGTTTCGACGCCATCTATTTTGGTGCCGTCGGCTGGCCGGATACCGTTCCGGACCATATTTCGTTG  >  NC_000913/1881925‑1882178

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A