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
A13 F1 I1 R1	778	68.7	3228504	93.4%	3015422	109.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,774,371	G→A	intergenic (+177/‑53)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,774,371	0	G	A	100.0%	143.2 / NA	45	intergenic (+177/‑53)	mtlA/mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (23/22); total (23/22)

CCTGATGCGCTACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGGAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGACGCGGGTATCCAA  >  NC_000913/3774237‑3774501

ccTGATGCGCTACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAaaaa                                                                                                                                >  2:826079/1‑139 (MQ=255)

   gATGCGCTACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGcc                                                                                                                             >  2:628226/1‑139 (MQ=255)

     tGCGCTACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTc                                                                                                                           >  2:877502/1‑139 (MQ=255)

          tACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCAcccc                                                                                                                      >  2:1072988/1‑139 (MQ=255)

              cTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGcc                                                                                                                  >  2:1529520/1‑139 (MQ=255)

               ttATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGccc                                                                                                                 <  1:1529520/139‑1 (MQ=255)

                 aTCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGAGAGGAAAAAGCCTCACCCCAGCCctc                                                                                                               >  2:377369/1‑139 (MQ=255)

                  tCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCctct                                                                                                              <  1:377542/139‑1 (MQ=255)

                       ccTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGt                                                                                                         <  2:1419051/139‑1 (MQ=255)

                         tACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTaa                                                                                                       <  1:628226/139‑1 (MQ=255)

                          aCAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTaaa                                                                                                      <  1:1072988/139‑1 (MQ=255)

                                tGCATCACAATTTGTTGCATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAACATCAtt                                                                                                >  1:1516473/1‑139 (MQ=255)

                                tGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACAtt                                                                                                >  1:238646/1‑139 (MQ=255)

                                tGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCAC‑GAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCctct                                                                                                              >  2:1279764/1‑124 (MQ=255)

                                tGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCAC‑GAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCctct                                                                                                              <  1:1279764/124‑1 (MQ=255)

                                  cATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATtga                                                                                              <  1:877502/139‑1 (MQ=255)

                                    tCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATtgatg                                                                                            <  2:705021/139‑1 (MQ=255)

                                    tCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATtgatg                                                                                            <  1:52197/139‑1 (MQ=255)

                                          tttGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGtt                                                                                      <  1:826079/139‑1 (MQ=255)

                                             gttgAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAAt                                                                                   <  2:238646/139‑1 (MQ=255)

                                               tgAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATAc                                                                                 >  2:125158/1‑139 (MQ=255)

                                                   tttGCACGTTCTTGTACGGCGGATAAGGTGTTTACGCCGCATCCGGCGCTGCGCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAATCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATTCTagg                                                                             <  1:377369/139‑3 (MQ=255)

                                                                      cGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgcg                                                          <  2:1508797/139‑1 (MQ=255)

                                                                        gATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGTTGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCa                                                        >  2:610786/1‑139 (MQ=255)

                                                                        gATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCa                                                        >  2:388990/1‑139 (MQ=255)

                                                                                          cATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           <  1:906497/118‑1 (MQ=255)

                                                                                          cATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           >  2:906497/1‑118 (MQ=255)

                                                                                                    tGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           >  1:124896/1‑108 (MQ=255)

                                                                                                    tGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           <  2:124896/108‑1 (MQ=255)

                                                                                                      ccccTCTCCTCACGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGTTGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTaaa                          <  1:610786/139‑1 (MQ=255)

                                                                                                                 aCGGAGAGGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTGAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGa               >  1:942529/1‑139 (MQ=255)

                                                                                                                     agagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATtgatg                                                                                            >  1:897450/1‑58 (MQ=255)

                                                                                                                     agagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATtgatg                                                                                            <  2:897450/58‑1 (MQ=255)

                                                                                                                     agagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGAcgcg           >  2:746733/1‑139 (MQ=255)

                                                                                                                     agagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGAcgcg           >  2:974013/1‑139 (MQ=255)

                                                                                                                      gagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCtt                                    <  2:684238/113‑1 (MQ=255)

                                                                                                                      gagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCtt                                    >  1:684238/1‑113 (MQ=255)

                                                                                                                      gagGGTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGACGCgg          >  2:1158126/1‑139 (MQ=255)

                                                                                                                        gggTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGt                                                                                       >  2:154187/1‑60 (MQ=255)

                                                                                                                        gggTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGt                                                                                       <  1:154187/60‑1 (MQ=255)

                                                                                                                        gggTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           >  2:1419438/1‑88 (MQ=255)

                                                                                                                        gggTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGgc                                                           <  1:1419438/88‑1 (MQ=255)

                                                                                                                        gggTTTGGGTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGACGCGGGt        >  2:352468/1‑139 (MQ=255)

                                                                                                                              gggTGAGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGACGCGGGTATCCaa  <  1:352468/139‑1 (MQ=255)

                                                                                                                                   aGGAAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGAcgc            <  2:1148463/124‑1 (MQ=255)

CCTGATGCGCTACGCTTATCAGGCCTACAGGATGCATCACAATTTGTTGAATTTGCACGTTCTTGTAGGCCGGATAAGGCGCTTACGCCGCATCCGGCGCTGCCCCTCTCCTCACGGAGAGGGTTTGGGTGAGGGAAAAGCCTCACCCCAGCCCTCTCGGGTAAAAACATTGATGAAGGTTAATACTATGAAAGCATTACATTTTGGCGCAGGTAATATCGGTCGTGGCTTTATCGGTAAACTGCTGGCAGACGCGGGTATCCAA  >  NC_000913/3774237‑3774501

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A