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 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,214,339	(C)_6→5	coding (306/1686 nt)	yehU ←	inner membrane putative sensory kinase in two‑component system with YehT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,214,334	0	C	.	100.0%	198.4 / NA	47	coding (311/1686 nt)	yehU	inner membrane putative sensory kinase in two‑component system with YehT
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (25/22); total (25/22)

GCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATGCCCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGAATCGTCAATGTGCAACCCAAAC  >  NC_000913/2214196‑2214468

gCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATGc                                                                                                                                           <  1:1097597/139‑1 (MQ=255)

       aCGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATGcccccatc                                                                                                                                    <  2:387840/139‑4 (MQ=255)

             cGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAatat                                                                                                                             <  1:843532/139‑1 (MQ=255)

                            tGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGccgccg                                                                                                           <  1:621701/139‑1 (MQ=255)

                                        cTTTATCAGTGCGTCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATGccc                                                                                                                                         <  1:641043/101‑1 (MQ=255)

                                        cTTTATCAGTGCGCCCGCGGCGGATCAGGGTGCTGTGTACCAGGCTACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATGccc                                                                                                                                         >  2:641043/1‑101 (MQ=255)

                                           tATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGc                                                                                            >  2:288538/1‑139 (MQ=255)

                                                           gcggATCAGGATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACgaccggac                                                                            >  2:143991/1‑139 (MQ=255)

                                                                    gATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAgc                                                                                                                <  1:295173/94‑1 (MQ=255)

                                                                    gATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAgc                                                                                                                >  2:295173/1‑94 (MQ=255)

                                                                      tGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACgaccgga                                                                             <  2:564684/127‑1 (MQ=255)

                                                                      tGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACgaccgga                                                                             >  1:564684/1‑127 (MQ=255)

                                                                      tGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAg                                                                 <  1:288538/139‑1 (MQ=255)

                                                                         tgtgTACCAGGCCACCGAGTAATACTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAgccg                                                              >  2:1067062/1‑139 (MQ=255)

                                                                                 aGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTAc                                                      <  1:143991/139‑1 (MQ=255)

                                                                                 aGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTAc                                                      >  2:1087730/1‑139 (MQ=255)

                                                                                  ggCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTAcc                                                     >  2:43471/1‑139 (MQ=255)

                                                                                  ggCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTAcc                                                     >  1:650283/1‑139 (MQ=255)

                                                                                  ggCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTAcc                                                     >  1:388943/1‑139 (MQ=255)

                                                                                   gCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACcg                                                    >  2:946815/1‑139 (MQ=255)

                                                                                     cACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACcgcg                                                  >  2:821063/1‑139 (MQ=255)

                                                                                       ccGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATGccc                                                                                                                                         <  2:133999/54‑1 (MQ=255)

                                                                                       ccGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATGccc                                                                                                                                         >  1:133999/1‑54 (MQ=255)

                                                                                       ccGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACgaccgga                                                                             >  1:1053925/1‑110 (MQ=255)

                                                                                       ccGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACgaccgga                                                                             <  2:1053925/110‑1 (MQ=255)

                                                                                       ccGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGcc                                                >  1:604062/1‑139 (MQ=255)

                                                                                       ccGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGcc                                                <  1:43471/139‑1 (MQ=255)

                                                                                        cGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTa                                                                                                                   <  2:307997/71‑1 (MQ=255)

                                                                                        cGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTa                                                                                                                   >  1:307997/1‑71 (MQ=255)

                                                                                            tAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCg                                           <  1:1067062/139‑1 (MQ=255)

                                                                                             aaTCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAgccgcc                                                            <  2:669428/121‑1 (MQ=255)

                                                                                             aaTCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAgccgcc                                                            >  1:669428/1‑121 (MQ=255)

                                                                                              aTCCTTCAACGATGGTCGAGATCATGCAGCTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCa                                         <  1:455739/139‑1 (MQ=255)

                                                                                              aTCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCa                                         <  2:243452/139‑1 (MQ=255)

                                                                                                   tCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGt                                    <  1:891981/139‑1 (MQ=255)

                                                                                                          tGGTCGAGATCATGCGACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCa                             >  1:787406/1‑139 (MQ=255)

                                                                                                          tGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCgg                                                                                                          >  1:275197/1‑62 (MQ=255)

                                                                                                          tGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCgg                                                                                                          <  2:275197/62‑1 (MQ=255)

                                                                                                          tGGTCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCa                             <  1:946815/139‑1 (MQ=255)

                                                                                                             tCGAGATCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATa                          >  1:298395/1‑139 (MQ=255)

                                                                                                                agaTCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGaa                       <  2:604062/139‑1 (MQ=255)

                                                                                                                 gaTCATGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGAAt                      <  1:821063/139‑1 (MQ=255)

                                                                                                                      tGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAAc                                                                                                >  2:186072/1‑60 (MQ=255)

                                                                                                                      tGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAAc                                                                                                <  1:186072/60‑1 (MQ=255)

                                                                                                                      tGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGAATCGTCa                 >  2:337482/1‑139 (MQ=255)

                                                                                                                      tGCAACTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGAATCGTCa                 >  1:410322/1‑139 (MQ=255)

                                                                                                                       gCAACTTAACGCGGTCATG‑CCCCCATCGAATATCGATGATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCa                                         <  2:931226/117‑1 (MQ=255)

                                                                                                                       gCAACTTAACGCGGTCATG‑CCCCCATCGAATATCGATGATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCa                                         >  1:931226/1‑117 (MQ=255)

                                                                                                                           cTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGAATCGTCAAtgtg            <  1:337482/139‑1 (MQ=255)

                                                                                                                           cTTAACGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGAATCGTCAAtgtg            <  2:733299/139‑1 (MQ=255)

                                                                                                                              aaCGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGAATCGTCAATGTGCaa         >  1:625512/1‑139 (MQ=255)

                                                                                                                              aaCGCGGTCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGAATCGTCAATGTGCaa         >  1:803147/1‑139 (MQ=255)

                                                                                                                                     tCATG‑CCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGAATCGTCAATGTGCAACCCAAAc  >  1:161912/1‑139 (MQ=255)

GCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATCCTTCAACGATGGTCGAGATCATGCAACTTAACGCGGTCATGCCCCCCATCGAATATC‑‑‑GATGTAAGCCGCCGGTCAGCCCAACCAGCCCACCGACGACCGGACCGCCGAGTAAGCCGCCCATTACCGCGCCTATCGCACGGGTATTGGCAATAGAATCGTCAATGTGCAACCCAAAC  >  NC_000913/2214196‑2214468

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `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