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
A3 F1 I2 R1	777	59.2	2955938	92.5%	2734242	106.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,569,410	T→C	D637G (GAT→GGT)	glgX ←	glycogen debranching enzyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,569,410	0	T	C	100.0%	163.5 / NA	46	D637G (GAT→GGT)	glgX	glycogen debranching enzyme
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (29/17); total (29/17)

TGGCGCGCCAACATTAAGTGATCGTTCTTCTCTAAACTAACCATGACTAACTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTATCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCGAGAGCAGAATTTGCAGCTGTTTCGGCCCGTTTTG  >  NC_000913/3569285‑3569543

tGGCGCGCCAACATTAAGTGATCGTTCTTCTCTAAACTAACCATGACTAACTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGaa                                                                                                                          <  1:84140/139‑1 (MQ=255)

                  tGATCGTTCTTCTCTAAACTAACCATGACTAACTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCa                                                                                                        >  2:194582/1‑139 (MQ=255)

                      cGTTCTTCTCTAAACTAACCATGACTAACTCTTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTcc                                                                                                    >  2:237471/1‑139 (MQ=255)

                      cGTTCTTCTCTAAACTAACCATGACTAACTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGc                                                                                                          >  1:792644/1‑133 (MQ=255)

                      cGTTCTTCTCTAAACTAACCATGACTAACTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGc                                                                                                          <  2:792644/133‑1 (MQ=255)

                      cGTTCTTCTCTAAACTAACCATGACTAACTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTcc                                                                                                    >  1:99652/1‑139 (MQ=255)

                                        ccATAACTAACTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCAGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCAGTCCCCAGCAGGTAAAACAAtc                                                                                  >  1:855023/1‑139 (MQ=255)

                                            gACTAACTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTg                                                                              >  2:1368078/1‑139 (MQ=255)

                                            gACTAACTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTg                                                                              >  2:867970/1‑139 (MQ=255)

                                                 aCTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAg                                                                                                                              <  2:17977/86‑1 (MQ=255)

                                                 aCTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAg                                                                                                                              >  1:17977/1‑86 (MQ=255)

                                                    ccTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTc                                                                                                     >  2:415359/1‑108 (MQ=255)

                                                    ccTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTc                                                                                                     <  1:415359/108‑1 (MQ=255)

                                                         tttATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGt                                                                 <  2:855023/139‑1 (MQ=255)

                                                               atcTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATggggg                                                                                                                    <  1:1001148/82‑1 (MQ=255)

                                                               atcTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATggggg                                                                                                                    >  2:1001148/1‑82 (MQ=255)

                                                               atcTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGtt                                                           >  1:869609/1‑139 (MQ=255)

                                                                      gAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCg                                                    <  2:99652/139‑1 (MQ=255)

                                                                           cacacaATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTg                                                      >  1:599724/1‑132 (MQ=255)

                                                                           cacacaATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTg                                                      <  2:599724/132‑1 (MQ=255)

                                                                           cacacaATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCaa                                               >  2:1130759/1‑139 (MQ=255)

                                                                            acacaATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCaaa                                              >  2:674069/1‑139 (MQ=255)

                                                                                aaTCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGc                                          >  1:21151/1‑139 (MQ=255)

                                                                                 aTCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCg                                         >  2:439958/1‑139 (MQ=255)

                                                                                  tCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGa                                        <  2:869609/139‑1 (MQ=255)

                                                                                      tgtgCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCg                                    >  2:1436268/1‑139 (MQ=255)

                                                                                      tgtgCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGAGTTAATTGCGATCAAAAAGCGATCCg                                    >  1:1231653/1‑139 (MQ=255)

                                                                                        tgCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCgag                                  >  2:1000966/1‑139 (MQ=255)

                                                                                          cAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCTGagag                                >  2:821773/1‑139 (MQ=255)

                                                                                             gTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGc                                                                                                          <  1:1205342/62‑1 (MQ=255)

                                                                                             gTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGc                                                                                                          >  2:1205342/1‑62 (MQ=255)

                                                                                             gTCCCTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCGAGAGCAg                             >  1:320347/1‑139 (MQ=255)

                                                                                                ccTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGt                                                                             >  2:1467482/1‑88 (MQ=255)

                                                                                                ccTGCCAGACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGt                                                                             <  1:1467482/88‑1 (MQ=255)

                                                                                                  tGCCAGACAGCCGTAATCGCTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACaa                                                                                    >  2:968086/1‑79 (MQ=255)

                                                                                                  tGCCAGACAGCCGTAATCACTGGGATACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACaa                                                                                    <  1:968086/79‑1 (MQ=255)

                                                                                                       gACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGc                                                                                                          >  1:978025/1‑52 (MQ=255)

                                                                                                       gACAGCCGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGc                                                                                                          <  2:978025/52‑1 (MQ=255)

                                                                                                            ccGTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCGAGAGCAGAATTTGCAGCTGttt              >  2:1150347/1‑139 (MQ=255)

                                                                                                              gTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCg                                                                                                             >  2:709802/1‑42 (MQ=255)

                                                                                                              gTAATCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCg                                                                                                             <  1:709802/42‑1 (MQ=255)

                                                                                                                 aTCACTGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCGAGAGCAGAATTTGCAGCTGTTTCGGcc         <  1:237471/139‑1 (MQ=255)

                                                                                                                      tGGGTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCGAGAGCAGAATTTGCAGCTGTTTCGGCCCGttt    <  2:21151/139‑1 (MQ=255)

                                                                                                                        ggTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCGAGAGCAGAATTTGCAGCTGTTTCGGCCCGTTTTg  >  2:1184771/1‑139 (MQ=255)

                                                                                                                         gTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCGAGAGCAGAATTTGCAGCTGTTTCGGCCCGttt    >  1:939602/1‑136 (MQ=255)

                                                                                                                         gTTACCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCGAGAGCAGAATTTGCAGCTGTTTCGGCCCGttt    <  2:939602/136‑1 (MQ=255)

TGGCGCGCCAACATTAAGTGATCGTTCTTCTCTAAACTAACCATGACTAACTCCTTTTTTATCATCTCTGGAACACACACAATCCGTGTGCAGGTCCCTGCCAGACAGCCGTAATCACTGGGTTATCCTCTCCAGCGAATGGGGGAATGGCGTGCCACTCCCCAGCAGGTAAAACAATCTCTGTTACCTCAAGCGTGGCGTTAATTGCGATCAAAAAGCGATCCGAGAGCAGAATTTGCAGCTGTTTCGGCCCGTTTTG  >  NC_000913/3569285‑3569543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A