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 I1 R1	770	68.5	3470224	91.7%	3182195	103.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,106,320	G→A	167 (TAG→TAA)	cpxP →	inhibitor of the cpx response, periplasmic adaptor protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,106,320	0	G	A	100.0%	198.3 / NA	61	167 (TAG→TAA)	cpxP	inhibitor of the cpx response, periplasmic adaptor protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (27/34); total (27/34)

CCTGTTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAGTAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACTAGCGTCAGTTGA  >  NC_000913/4106185‑4106454

ccTGTTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAAGTCACGTTCCCAGtaataa                                                                                                                                      >  1:1167719/1‑139 (MQ=255)

   gTTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAAcc                                                                                                                                   >  1:464137/1‑139 (MQ=255)

      aaCGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTg                                                                                                                                <  1:500174/139‑1 (MQ=255)

        cGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGCGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGtt                                                                                                                              >  1:545802/1‑139 (MQ=255)

            ggAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                                          >  2:845682/1‑139 (MQ=255)

            ggAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                                          <  2:419554/139‑1 (MQ=255)

            ggAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTcc                                                                                                                          <  1:609447/139‑1 (MQ=255)

              agcagcAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCt                                                                                                                         >  1:1135792/1‑138 (MQ=255)

              agcagcAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCt                                                                                                                         <  2:1135792/138‑1 (MQ=255)

                  gcaAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCa                                                                                                                    <  2:981215/139‑1 (MQ=255)

                  gcaAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCa                                                                                                                    <  2:772720/139‑1 (MQ=255)

                   caAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCAt                                                                                                                   >  1:1396023/1‑139 (MQ=255)

                        ggTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGaca                                                                                                              >  2:502859/1‑139 (MQ=255)

                         gTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGacac                                                                                                             <  1:502859/139‑1 (MQ=255)

                          ttttAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACAcc                                                                                                            >  1:592699/1‑139 (MQ=255)

                                   agaAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTc                                                                                                   <  1:845682/139‑1 (MQ=255)

                                     aaaCATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCtt                                                                                                 <  2:464137/139‑1 (MQ=255)

                                              caacGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCCATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACAt                                                                                        >  2:1446669/1‑139 (MQ=255)

                                                       gAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTgggg                                                                               <  2:1396023/139‑1 (MQ=255)

                                                         gCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑t                                                                            <  2:592699/139‑1 (MQ=255)

                                                          cAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑tt                                                                           >  2:1716399/1‑139 (MQ=255)

                                                             ttGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATa                                                                                                                  >  1:293365/1‑98 (MQ=255)

                                                             ttGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATa                                                                                                                  <  2:293365/98‑1 (MQ=255)

                                                             ttGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGacac                                                                                                             >  2:107469/1‑103 (MQ=255)

                                                             ttGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGacac                                                                                                             <  1:107469/103‑1 (MQ=255)

                                                               gCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑ttttttt                                                                      <  2:363045/139‑1 (MQ=255)

                                                                               tGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGc                                                        <  1:1043835/137‑1 (MQ=255)

                                                                               tGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGc                                                        >  2:1043835/1‑137 (MQ=255)

                                                                               tGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACATTCCCAGTAATAAACCCTGTTTTcc                                                                                                                          <  2:1163804/72‑1 (MQ=255)

                                                                               tGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACATTCCCAGTAATAAACCCTGTTTTcc                                                                                                                          >  1:1163804/1‑72 (MQ=255)

                                                                                 gCAAAACAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAAGCCTGTTTTCCTTGCCATAGACACCATCCCTGTGTTCCCCCACATGCTGTGGGGGTTTTTTTTTATCCTCAGTTTGTctg                                                     <  2:138018/139‑1 (MQ=255)

                                                                                  cAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGcc                                                                                                                     <  1:1310272/74‑1 (MQ=255)

                                                                                  cAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGcc                                                                                                                     >  2:1310272/1‑74 (MQ=255)

                                                                                  cAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctgct                                                   <  2:1167719/139‑1 (MQ=255)

                                                                                           tCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGc                                          >  1:1252817/1‑139 (MQ=255)

                                                                                            cATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCa                                         <  1:1716399/139‑1 (MQ=255)

                                                                                                         aTTGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGAttt                            >  1:354555/1‑139 (MQ=255)

                                                                                                           tGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGc                          <  1:1306033/139‑1 (MQ=255)

                                                                                                           tGAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGc                          <  2:1252817/139‑1 (MQ=255)

                                                                                                            gAGTTGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTAGCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCt                         <  2:545802/139‑1 (MQ=255)

                                                                                                            gAGTAGTAGCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCt                         <  1:1446669/139‑1 (MQ=255)

                                                                                                               tagtagCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTcc                      >  2:1346259/1‑139 (MQ=255)

                                                                                                                agtagCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCcaca                                                                                         >  2:510571/1‑72 (MQ=255)

                                                                                                                agtagCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCcaca                                                                                         <  1:510571/72‑1 (MQ=255)

                                                                                                                  tagCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCca                                                                                           >  2:1621389/1‑68 (MQ=255)

                                                                                                                  tagCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCca                                                                                           <  1:1621389/68‑1 (MQ=255)

                                                                                                                    gCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTgctgct                                                <  2:237025/108‑1 (MQ=255)

                                                                                                                    gCAACTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTgctgct                                                >  1:237025/1‑108 (MQ=255)

                                                                                                                       aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCt                                                                >  1:721125/1‑89 (MQ=255)

                                                                                                                       aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCt                                                                <  2:721125/89‑1 (MQ=255)

                                                                                                                       aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGcc                                                       >  2:232485/1‑98 (MQ=255)

                                                                                                                       aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGcc                                                       <  1:232485/98‑1 (MQ=255)

                                                                                                                       aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACt              >  2:1693313/1‑139 (MQ=255)

                                                                                                                       aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACt              <  2:354555/139‑1 (MQ=255)

                                                                                                                       aCTCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACt              >  2:745427/1‑139 (MQ=255)

                                                                                                                         tCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                                     <  1:357622/98‑1 (MQ=255)

                                                                                                                         tCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCctg                                                     >  2:357622/1‑98 (MQ=255)

                                                                                                                         tCACGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACTAg            <  1:1693313/139‑1 (MQ=255)

                                                                                                                            cGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCtt                                                                                                 >  2:1709273/1‑52 (MQ=255)

                                                                                                                            cGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCtt                                                                                                 <  1:1709273/52‑1 (MQ=255)

                                                                                                                            cGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTgctgct                                                >  1:1399124/1‑100 (MQ=255)

                                                                                                                            cGTTCCCAGTAATAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTgctgct                                                <  2:1399124/100‑1 (MQ=255)

                                                                                                                                   agtaatAAACCCTGTTTTCCTTGCCATAGACACCATCCCt                                                                                                      >  1:1411762/1‑40 (MQ=255)

                                                                                                                                   agtaatAAACCCTGTTTTCCTTGCCATAGACACCATCCCt                                                                                                      <  2:1411762/40‑1 (MQ=255)

                                                                                                                                   agtaatAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCt                         <  1:968718/116‑1 (MQ=255)

                                                                                                                                   agtaatAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCt                         >  2:968718/1‑116 (MQ=255)

                                                                                                                                   agtaatAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACTAGCGTCAGTTGa  >  1:806429/1‑139 (MQ=255)

CCTGTTAACGCCGGAGCAGCAAGCGGTTTTAAACGAGAAACATCAACAACGAATGGAGCAGTTGCGTGACGTGACGCAATGGCAAAAAAGTTCATCGTTGAAGCTATTGAGTAGTAGCAACTCACGTTCCCAGTAGTAAACCCTGTTTTCCTTGCCATAGACACCATCCCTGTCTTCCCCCACATGCTGTGGGGG‑TTTTTTTTATCCTCAATTTGCCTGCTGCTTAATGCATTGCAGATGATTTGCTTCCGTTATACTAGCGTCAGTTGA  >  NC_000913/4106185‑4106454

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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