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
A13 F1 I1 R1	778	68.7	3228504	93.4%	3015422	109.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,549,088	G→A	G94E (GGG→GAG)	fimH →	minor component of type 1 fimbriae

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,549,088	0	G	A	100.0%	143.3 / NA	45	G94E (GGG→GAG)	fimH	minor component of type 1 fimbriae
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (19/26); total (19/26)

GTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGCCGTGGCCGGTGGCGCTTTATTTGACGCCTGTGAGCAGTGCGGGCGG  >  NC_000913/4548952‑4549220

gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCgaga                                                                                                                                    <  1:144661/139‑1 (MQ=255)

gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCgaga                                                                                                                                    <  1:1482257/139‑1 (MQ=255)

gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCgaga                                                                                                                                    <  2:498247/139‑1 (MQ=255)

gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCgaga                                                                                                                                    <  1:263715/139‑1 (MQ=255)

gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCgaga                                                                                                                                    <  2:291160/139‑1 (MQ=255)

    aTGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGt                                                                                                                                <  1:452999/139‑1 (MQ=255)

     tgtgGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTa                                                                                                                               <  1:422495/139‑1 (MQ=255)

         gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAat                                                                                                                           >  1:1388951/1‑139 (MQ=255)

           gCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAatat                                                                                                                         <  2:348274/139‑1 (MQ=255)

           gCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAatat                                                                                                                         <  2:1161959/139‑1 (MQ=255)

              aaaCCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACCGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGt                                                                                                                      <  2:969816/139‑1 (MQ=255)

                 ccTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGc                                                                                                                   >  2:1319183/1‑139 (MQ=255)

                   tGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAg                                                                                                                 <  2:853143/139‑1 (MQ=255)

                      tCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAg                                                                                                              <  2:1265468/139‑1 (MQ=255)

                      tCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAg                                                                                                              <  1:477921/139‑1 (MQ=255)

                           gATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAAtata                                                                                                                        <  1:742236/124‑1 (MQ=255)

                           gATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAAtata                                                                                                                        >  2:742236/1‑124 (MQ=255)

                            aTCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATcc                                                                                                        <  1:997051/139‑1 (MQ=255)

                              cTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCAt                                                                                                      <  2:29064/139‑1 (MQ=255)

                               tttCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTa                                                                                                           >  2:463601/1‑133 (MQ=255)

                               tttCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTa                                                                                                           <  1:463601/133‑1 (MQ=255)

                                        aaaTCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTaccac                                                                                            <  1:1319183/139‑1 (MQ=255)

                                                          aTTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCgt                                                                          <  1:73066/139‑1 (MQ=255)

                                                            tATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCgttg                                                                        >  1:887598/1‑139 (MQ=255)

                                                                  gAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTAt                                                                                                          >  1:1075359/1‑99 (MQ=255)

                                                                  gAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTAt                                                                                                          <  2:1075359/99‑1 (MQ=255)

                                                                         ttACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCt                                                                                                 >  1:1582015/1‑101 (MQ=255)

                                                                         ttACAGACTATGTCACACTGCAACGAGGCGCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCt                                                                                                 <  2:1582015/101‑1 (MQ=255)

                                                                           aCAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGaa                                                         >  1:367859/1‑139 (MQ=255)

                                                                                         acTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGcc                                               <  1:1270403/135‑1 (MQ=255)

                                                                                         acTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGcc                                               >  2:1270403/1‑135 (MQ=255)

                                                                                           tGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGCCGTGGcc                                         >  1:173453/1‑139 (MQ=255)

                                                                                             cAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCAt                                                                                                      >  2:339208/1‑76 (MQ=255)

                                                                                             cAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCAt                                                                                                      <  1:339208/76‑1 (MQ=255)

                                                                                                cGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTta                                                                    >  1:624901/1‑107 (MQ=255)

                                                                                                cGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTta                                                                    <  2:624901/107‑1 (MQ=255)

                                                                                                     cTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGcc                                               >  1:739333/1‑123 (MQ=255)

                                                                                                     cTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGcc                                               <  2:739333/123‑1 (MQ=255)

                                                                                                     cTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGCCGTGGCCGGTGGCGCtt                               >  1:619242/1‑139 (MQ=255)

                                                                                                            tATGGCGGCGTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGCCGTGGCCGGTGGCGCTTTATTTGa                        <  1:726552/139‑1 (MQ=255)

                                                                                                                    cgTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCcgcgcg                                                                           >  2:1193414/1‑80 (MQ=255)

                                                                                                                    cgTGTTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCcgcgcg                                                                           <  1:1193414/80‑1 (MQ=255)

                                                                                                                      tgtTATCTAATTTTTCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGCCGTGGCCGGTGGCGCTTTATTTGACGCCTGTGAg              <  2:367859/139‑1 (MQ=255)

                                                                                                                                tttttCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTaccac                                                                                            <  1:21374/51‑1 (MQ=255)

                                                                                                                                tttttCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTaccac                                                                                            >  2:21374/1‑51 (MQ=255)

                                                                                                                                tttttCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAg                                                 >  1:149514/1‑94 (MQ=255)

                                                                                                                                tttttCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAg                                                 <  2:149514/94‑1 (MQ=255)

                                                                                                                                  tttCCGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGCCGTGGCCGGTGGCGCTTTATTTGACGCCTGTGAGCAGTgcgggcgg  >  1:464601/1‑139 (MQ=255)

                                                                                                                                     ccGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGaa                                                         <  2:317571/81‑1 (MQ=255)

                                                                                                                                     ccGAGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGaa                                                         >  1:317571/1‑81 (MQ=255)

GTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGATAAGCCGTGGCCGGTGGCGCTTTATTTGACGCCTGTGAGCAGTGCGGGCGG  >  NC_000913/4548952‑4549220

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A