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
A2 F1 I1 R1	81	28.9	1316934	95.8%	1261622	113.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,482,862	A→G	L160L (TTA→CTA)	emrK ←	multidrug resistance efflux pump membrane fusion protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,482,862	0	A	G	100.0%	116.8 / NA	32	L160L (TTA→CTA)	emrK	multidrug resistance efflux pump membrane fusion protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/16); total (16/16)

GCCAACCAGGCTTCTTTAGTTGCATCCGCCGCTTCAACGACTTGTGGCTGACGGTTTAATGGTGTGTTCATTACTAAAGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGCGACTTCGGCACTGTATTGTTTAT  >  NC_000913/2482726‑2482996

gcCAACCAGGCTTCTTTAGTTGCATCCGCCGCTTCAACGACTTGTGGCTGACGGTTTAATGGTGTGTTCATTACTAAAGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCg                                                                                                                                      <  1:259880/139‑1 (MQ=255)

gcCAACCAGGCTTCTTTAGTTGCATCCGCCGCTTCAACGACTTGTGGCTGACGGTTTAATGGTGTGTTCATTACTAAAGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCg                                                                                                                                      <  1:286544/139‑1 (MQ=255)

          cttcttTAGTTGCATCCGCCGCTTCAACGACTTGTGGCTGACGGTTTAATGGTGTGTTCATTACTAAAGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGt                                                                                                                            <  2:541308/139‑1 (MQ=255)

              tttAGTTGCATCCGCCGCTTCAACGACTTGTGGCTGACGGTTTAATGGTGTGTTCATTACTAAAGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGc                                                                                                                        >  2:31882/1‑139 (MQ=255)

                     gCATCCGCCGCTTCAACGACTTGTGGCTGACGGTTTAATGGTGTGTTCATTACTAAAGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCg                                                                                                                 <  2:247592/139‑1 (MQ=255)

                       aTCCGCCGCTTCAACGACTTGTGGCTGACGGTTTAATGGTGTGTTCATTACTAAAGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGtt                                                                                                               >  1:422099/1‑139 (MQ=255)

                                                                  ttCATTACTAAAGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGt                                                                    >  1:250857/1‑139 (MQ=255)

                                                                            aaGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGt                                                                                                                >  1:315485/1‑85 (MQ=255)

                                                                            aaGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGt                                                                                                                <  2:315485/85‑1 (MQ=255)

                                                                            aaGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCg                                                                         >  1:276613/1‑124 (MQ=255)

                                                                            aaGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCg                                                                         <  2:276613/124‑1 (MQ=255)

                                                                            aaGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGa                                                                        <  2:528141/125‑1 (MQ=255)

                                                                            aaGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGa                                                                        >  1:528141/1‑125 (MQ=255)

                                                                            aaGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAAtcttc                                                          >  1:244391/1‑139 (MQ=255)

                                                                            aaGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAAtcttc                                                          >  2:37881/1‑139 (MQ=255)

                                                                                                 ccTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAAt                                     <  2:250857/139‑1 (MQ=255)

                                                                                                   tGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATAc                                   >  1:514368/1‑139 (MQ=255)

                                                                                                          cGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGAttgt                                                >  2:114691/1‑119 (MQ=255)

                                                                                                          cGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGAttgt                                                <  1:114691/119‑1 (MQ=255)

                                                                                                          cGGCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGa                            >  2:354848/1‑139 (MQ=255)

                                                                                                           ggCATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGaa                           <  1:53626/139‑1 (MQ=255)

                                                                                                             cATTCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGc                         <  2:514368/139‑1 (MQ=255)

                                                                                                               ttCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTtata                                                                <  2:300977/98‑1 (MQ=255)

                                                                                                               ttCAATGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTtata                                                                >  1:300977/1‑98 (MQ=255)

                                                                                                                    tGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGCGACTTCg                  <  2:556497/139‑1 (MQ=255)

                                                                                                                    tGCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGCGACTTCg                  >  1:556497/1‑139 (MQ=255)

                                                                                                                     gCCGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGCGACTTCgg                 <  1:354848/139‑1 (MQ=255)

                                                                                                                       cGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGCGACTTCGGCa               <  2:172326/139‑1 (MQ=255)

                                                                                                                       cGCTTTGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGCGACTTCGGCa               >  2:119860/1‑139 (MQ=255)

                                                                                                                          tttGCTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGCGACTTCGGCACTg            >  2:407184/1‑139 (MQ=255)

                                                                                                                              cTACTTATTAGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGCGACTTCGGCACTGTAtt        >  1:339103/1‑139 (MQ=255)

                                                                                                                                    attaGCGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGCGACTTCGGCACTGTATTGTTTAt  <  1:213205/139‑1 (MQ=255)

GCCAACCAGGCTTCTTTAGTTGCATCCGCCGCTTCAACGACTTGTGGCTGACGGTTTAATGGTGTGTTCATTACTAAAGCTTTATTCGCTTTATAAGCCTGGATAGCGGCATTCAATGCCGCTTTGCTACTTATTAACGTATCTTTGGTATGCTCCAGCGTTTCTTTTGAAATAACCCCCTGCTTCGCTAACGGCACTCGACGGTTATAATCTTCTAAAGATTGTTGATACTGAATACGTGCTGAAGCGACTTCGGCACTGTATTGTTTAT  >  NC_000913/2482726‑2482996

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A