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	1,673,314	A→G	L63P (CTG→CCG)	mdtJ ←	multidrug efflux system transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,673,314	0	A	G	100.0%	154.0 / NA	43	L63P (CTG→CCG)	mdtJ	multidrug efflux system transporter
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (22/21); total (22/21)

ACGGGTACCTGATTTTATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCG  >  NC_000913/1673181‑1673446

aCGGGTACCTGATTTTATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCa                                                                                                                                 <  1:64772/139‑1 (MQ=255)

  gggTACCTGATTTTATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATa                                                                                                                               >  1:123782/1‑139 (MQ=255)

       ccTGATTTTATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTa                                                                                                                          >  1:1011069/1‑139 (MQ=255)

       ccTGATTTTATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTa                                                                                                                          >  2:37698/1‑139 (MQ=255)

               tATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGgcgc                                                                                                                                  <  1:133949/123‑1 (MQ=255)

               tATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGgcgc                                                                                                                                  >  2:133949/1‑123 (MQ=255)

                     cacaATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGAtt                                                                                                            >  1:404722/1‑139 (MQ=255)

                         aTCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGAtttttt                                                                                                        >  2:507267/1‑139 (MQ=255)

                          tCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGAttttttt                                                                                                       >  1:975793/1‑139 (MQ=255)

                            ccGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTaa                                                                                                     <  1:274110/139‑1 (MQ=255)

                             cgccGACCAGGATGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCAAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAAc                                                                                                    >  2:612107/4‑139 (MQ=255)

                                cGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGc                                                                                                 >  2:1047673/1‑139 (MQ=255)

                                   ccAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGaa                                                                                              <  1:1047673/139‑1 (MQ=255)

                                      gggTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAaga                                                                                           <  2:975793/139‑1 (MQ=255)

                                      gggTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAaga                                                                                           <  2:864528/139‑1 (MQ=255)

                                       ggtggtTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAagag                                                                                          <  1:37698/139‑1 (MQ=255)

                                           gtTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGaa                                                                                      <  1:507267/139‑1 (MQ=255)

                                                cccGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAatata                                                                                 <  2:123782/139‑1 (MQ=255)

                                                cccGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAatata                                                                                 <  1:986178/139‑1 (MQ=255)

                                                   ggCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATAc                                                                              >  1:408940/1‑139 (MQ=255)

                                                                    aTAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAc                                                             <  1:348563/139‑1 (MQ=255)

                                                                                   ataacataacGCTAAAATAGGTATAAAATAAAGTACCAATCCCTTCCCACGGCCCATAGGCTAATGCTAAGGCGATTTTTTTAAATGCAAATGATAGAAATAGAGACGACAGAGAAATCATCACCTTCATTAAAATaaa                                              <  2:746077/139‑1 (MQ=255)

                                                                                   aTAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAATCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAcc                                                            <  2:720229/125‑1 (MQ=255)

                                                                                   aTAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAcc                                                            >  1:720229/1‑125 (MQ=255)

                                                                                            cGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAcc                                                            <  1:554104/116‑1 (MQ=255)

                                                                                            cGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAcc                                                            >  2:554104/1‑116 (MQ=255)

                                                                                               tAAACAAGGTAATAAATAAAATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTcc                                  >  2:385714/1‑139 (MQ=255)

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

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

                                                                                                           taaataaaATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGTCGATTTTTTTAACGGCGAAAGAGAGAAatata                                                                                 <  1:186390/80‑1 (MQ=255)

                                                                                                           taaataaaATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAgagaga                                                                                       >  1:510020/1‑74 (MQ=255)

                                                                                                           taaataaaATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAgagaga                                                                                       <  2:510020/74‑1 (MQ=255)

                                                                                                           taaataaaATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAatata                                                                                 >  2:186390/1‑80 (MQ=255)

                                                                                                           taaataaaATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTccc                                 <  2:566951/128‑1 (MQ=255)

                                                                                                           taaataaaATACCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTccc                                 >  1:566951/1‑128 (MQ=255)

                                                                                                                 aaataCCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGaaa                                                                                             >  2:631945/1‑62 (MQ=255)

                                                                                                                 aaataCCGATACCTTCCCACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGaaa                                                                                             <  1:631945/62‑1 (MQ=255)

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

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

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

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

                                                                                                                                 ccACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAagagag                                                                                        >  2:46371/1‑51 (MQ=255)

                                                                                                                                 ccACGGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAagagag                                                                                        <  1:46371/51‑1 (MQ=255)

ACGGGTACCTGATTTTATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCG  >  NC_000913/1673181‑1673446

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