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
A10 F1 I1 R1	759	65.2	3386260	90.7%	3071337	101.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	850,389	T→C	intergenic (‑292/‑61)	rhtA ← / → ompX	threonine and homoserine efflux system/outer membrane protein X

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	850,389	0	T	C	100.0%	133.5 / NA	38	intergenic (‑292/‑61)	rhtA/ompX	threonine and homoserine efflux system/outer membrane protein X
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/19); total (19/19)

TGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGAC  >  NC_000913/850259‑850523

tgaCAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAtt                                                                                                                                  <  1:1525893/137‑1 (MQ=255)

tgaCAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAtt                                                                                                                                  >  2:1525893/1‑137 (MQ=255)

                         tACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGTGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGa                                                                                                       >  1:1327849/1‑139 (MQ=255)

                          aCGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                 >  1:276205/1‑128 (MQ=255)

                          aCGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                 <  2:276205/128‑1 (MQ=255)

                          aCGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGAc                                                                                                      >  2:153492/1‑139 (MQ=255)

                                      gAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATca                                                                                          >  2:642403/1‑139 (MQ=255)

                                                                        tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            >  2:1238006/1‑103 (MQ=255)

                                                                        tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            <  1:1238006/103‑1 (MQ=255)

                                                                        tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCt                                                        >  1:434914/1‑139 (MQ=255)

                                                                               aCGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCa                                                 <  2:883740/139‑1 (MQ=255)

                                                                                cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                        >  2:1006906/1‑67 (MQ=255)

                                                                                cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                        <  1:1006906/67‑1 (MQ=255)

                                                                                cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGAc                                                                                                      >  2:271404/1‑85 (MQ=255)

                                                                                cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGAc                                                                                                      <  1:271404/85‑1 (MQ=255)

                                                                                  ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAtt                                                                                                                                  >  1:380334/1‑55 (MQ=255)

                                                                                  ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAtt                                                                                                                                  <  2:380334/55‑1 (MQ=255)

                                                                                  ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            >  2:978838/1‑93 (MQ=255)

                                                                                  ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            <  1:978838/93‑1 (MQ=255)

                                                                                    cTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGAc                                                                                                      >  1:938962/1‑81 (MQ=255)

                                                                                    cTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGc                                            >  1:243297/1‑139 (MQ=255)

                                                                                    cTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGACATATTTAAAACTTAGGAc                                                                                                      <  2:938962/81‑1 (MQ=255)

                                                                                      gTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCg                                          <  1:642403/139‑1 (MQ=255)

                                                                                                 tGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACt                                                                                                     >  2:1030418/1‑69 (MQ=255)

                                                                                                 tGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTCGATATATTTAAAACTTAGGACt                                                                                                     <  1:1030418/69‑1 (MQ=255)

                                                                                                    cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCg                                          >  2:763542/1‑125 (MQ=255)

                                                                                                    cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCg                                          <  1:763542/125‑1 (MQ=255)

                                                                                                       gTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCAcc                         <  2:1327849/139‑1 (MQ=255)

                                                                                                        ttAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCg                        >  2:1535387/1‑139 (MQ=255)

                                                                                                        ttAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCg                        >  1:766935/1‑139 (MQ=255)

                                                                                                           gACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAg                     <  1:1535387/139‑1 (MQ=255)

                                                                                                             cATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATg                                                           <  1:551853/99‑1 (MQ=255)

                                                                                                             cATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATg                                                           >  2:551853/1‑99 (MQ=255)

                                                                                                               tCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTAc                 <  2:243297/139‑1 (MQ=255)

                                                                                                                       cgcgAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAgg                    >  1:590184/1‑128 (MQ=255)

                                                                                                                       cgcgAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAgg                    <  2:590184/128‑1 (MQ=255)

                                                                                                                           aaGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGc     <  1:1026299/139‑1 (MQ=255)

                                                                                                                              agTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGAc  <  2:11259/139‑1 (MQ=255)

TGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGAC  >  NC_000913/850259‑850523

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A