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
A14 F1 I2 R1	774	49.2	2112398	96.9%	2046913	118.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,673,416	T→C	E29G (GAG→GGG)	mdtJ ←	multidrug efflux system transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,673,416	0	T	C	100.0%	190.8 / NA	53	E29G (GAG→GGG)	mdtJ	multidrug efflux system transporter
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (31/22); total (31/22)

GTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGA  >  NC_000913/1673284‑1673550

gTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGa                                                                                                                                  >  1:541386/1‑139 (MQ=255)

  aataaataAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACg                                                                                                                                <  2:408940/139‑1 (MQ=255)

           aataCCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCAt                                                                                                                       >  1:448725/1‑139 (MQ=255)

                cGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCAt                                                                                                                  >  1:653378/1‑139 (MQ=255)

                cGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCAt                                                                                                                  >  1:882133/1‑139 (MQ=255)

                        tCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCg                                                                                                          <  2:1011069/139‑1 (MQ=255)

                               gcgcATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGt                                                                                                   <  1:385714/139‑1 (MQ=255)

                                cgcATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTa                                                                                                  >  1:877667/1‑139 (MQ=255)

                                  cATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAAt                                                                                                >  2:295671/1‑139 (MQ=255)

                                   aTAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGAAGCTCGCCCATTTCATTGACAGCGTACCGGTAAtt                                                                                               >  1:843954/1‑139 (MQ=255)

                                          aCGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAg                                                                                        >  2:1014528/1‑139 (MQ=255)

                                                 aGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGc                                                                                 >  1:447796/1‑139 (MQ=255)

                                                  ggCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGcc                                                                                <  2:447796/139‑1 (MQ=255)

                                                  ggCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGcc                                                                                >  1:661826/1‑139 (MQ=255)

                                                     gATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGa                                                                             <  2:541386/139‑1 (MQ=255)

                                                       tttttttAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGAcc                                                                           <  2:661826/139‑1 (MQ=255)

                                                       tttttttAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGAcc                                                                           >  2:672609/1‑139 (MQ=255)

                                                                    gAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCaa                                                              <  2:882133/139‑1 (MQ=255)

                                                                    gAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCaa                                                              <  1:295671/139‑1 (MQ=255)

                                                                    gAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCaa                                                              <  2:448725/139‑1 (MQ=255)

                                                                           agaAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAatat                                                       >  1:710970/1‑139 (MQ=255)

                                                                               atatatACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACAt                                                   <  2:404722/139‑1 (MQ=255)

                                                                               atatatACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACAt                                                   <  2:877667/139‑1 (MQ=255)

                                                                                  tataCGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGt                                                >  2:449303/1‑139 (MQ=255)

                                                                                   ataCGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTc                                               >  1:1034138/1‑139 (MQ=255)

                                                                                     aCGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTc                                                                                                                             >  2:151130/1‑59 (MQ=255)

                                                                                     aCGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTc                                                                                                                             <  1:151130/59‑1 (MQ=255)

                                                                                     aCGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCt                                             >  2:711364/1‑139 (MQ=255)

                                                                                     aCGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCt                                             <  1:1014528/139‑1 (MQ=255)

                                                                                     aCGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCt                                             >  2:268484/1‑139 (MQ=255)

                                                                                          agagAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTg                                                                                           <  1:404481/88‑1 (MQ=255)

                                                                                          agagAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTg                                                                                           >  2:404481/1‑88 (MQ=255)

                                                                                          agagAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTcc                                        >  1:40901/1‑139 (MQ=255)

                                                                                            agaAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGccc                                                                                                                         <  1:573944/56‑1 (MQ=255)

                                                                                            agaAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGccc                                                                                                                         >  2:573944/1‑56 (MQ=255)

                                                                                            agaAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTg                                      <  2:418056/139‑1 (MQ=255)

                                                                                            agaAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTg                                      >  1:952756/1‑139 (MQ=255)

                                                                                            agaAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTg                                      >  2:248354/1‑139 (MQ=255)

                                                                                            agaAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTg                                      >  1:795273/1‑139 (MQ=255)

                                                                                                 tcatcaCCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGccc                                                                                                                         >  1:71911/1‑51 (MQ=255)

                                                                                                 tcatcaCCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGccc                                                                                                                         <  2:71911/51‑1 (MQ=255)

                                                                                                   atcaCCAGCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAgaga                               >  2:701644/1‑139 (MQ=255)

                                                                                                          gCATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTAttt                        >  1:754720/1‑139 (MQ=255)

                                                                                                           cATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCa                                                                                      <  1:738521/76‑1 (MQ=255)

                                                                                                           cATTAAAATAAAGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCa                                                                                      >  2:738521/1‑76 (MQ=255)

                                                                                                                      aGCCGCCATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCtt            >  1:376161/1‑139 (MQ=255)

                                                                                                                        ccgccATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGt                                                                                                   <  2:356382/50‑1 (MQ=255)

                                                                                                                        ccgccATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGt                                                                                                   >  1:356382/1‑50 (MQ=255)

                                                                                                                           ccATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCtaa                                                                        <  1:888938/74‑1 (MQ=255)

                                                                                                                           ccATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCtaa                                                                        >  2:888938/1‑74 (MQ=255)

                                                                                                                           ccATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCaata                                                            <  1:846942/86‑1 (MQ=255)

                                                                                                                           ccATTTCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCaata                                                            >  2:846942/1‑86 (MQ=255)

                                                                                                                                tCCCCCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGa  <  1:268484/139‑1 (MQ=255)

GTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGA  >  NC_000913/1673284‑1673550

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