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
A10 F1 I2 R1	67	36.0	1614110	95.1%	1535018	114.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,471,819	A→G	pseudogene (304/579 nt)	yfdL ←	pseudogene, CPS‑53 (KpLE1) prophage,Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,471,819	0	A	G	100.0%	167.5 / NA	44	pseudogene (304/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage,Phage or Prophage Related
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (21/23); total (21/23)

CCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCGTGCCGTCCAATTTGATATCGCCAAACGGAT  >  NC_000913/2471688‑2471950

ccGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATa                                                                                                                              >  2:622204/1‑139 (MQ=255)

   cAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATaaaa                                                                                                                           <  2:343581/139‑1 (MQ=255)

        aTCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTAcc                                                                                                                      <  2:243086/139‑1 (MQ=255)

             ttCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCatat                                                                                                                 <  1:697055/139‑1 (MQ=255)

               cGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCa                                                                                                               <  1:38995/139‑1 (MQ=255)

                ggAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAg                                                                                                              >  1:58127/1‑139 (MQ=255)

                     tGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCa                                                                                                                                >  2:375103/1‑116 (MQ=255)

                     tGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCa                                                                                                                                <  1:375103/116‑1 (MQ=255)

                            ggAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCa                                                                                                                                >  2:551422/1‑109 (MQ=255)

                            ggAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCa                                                                                                                                <  1:551422/109‑1 (MQ=255)

                            ggAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCg                                                                                                  >  2:401344/1‑139 (MQ=255)

                                aaTAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGcccc                                                                                              <  1:401344/139‑1 (MQ=255)

                                aaTAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGcccc                                                                                              <  2:740066/139‑1 (MQ=255)

                                    ggTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTc                                                                                          <  1:70335/139‑1 (MQ=255)

                                          tgtgTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACa                                                                                    <  2:297327/139‑1 (MQ=255)

                                              tCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTc                                                                                >  1:551125/1‑139 (MQ=255)

                                                        tCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTAcc                                                                                                                      <  2:31836/91‑1 (MQ=255)

                                                        tCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTAcc                                                                                                                      >  1:31836/1‑91 (MQ=255)

                                                        tCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCata                                                                                                                  <  1:84740/95‑1 (MQ=255)

                                                        tCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCata                                                                                                                  >  2:84740/1‑95 (MQ=255)

                                                        tCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGc                                                                      >  1:123353/1‑139 (MQ=255)

                                                        tCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGc                                                                      >  2:408298/1‑139 (MQ=255)

                                                        tCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGc                                                                      >  2:340411/1‑139 (MQ=255)

                                                              gAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTcc                                                                <  1:408298/139‑1 (MQ=255)

                                                                 cATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTAcc                                                                                                                      <  2:404393/82‑1 (MQ=255)

                                                                 cATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTAcc                                                                                                                      >  1:404393/1‑82 (MQ=255)

                                                                                 ttGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCgaga                                             <  1:340411/139‑1 (MQ=255)

                                                                                         ttAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTg                                     >  1:620628/1‑139 (MQ=255)

                                                                                              ccGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCg                                >  2:290899/1‑139 (MQ=255)

                                                                                              ccGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCg                                >  1:611566/1‑139 (MQ=255)

                                                                                                 gATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGTGAGCCTTTTGCACCGTGc                             >  1:297332/1‑139 (MQ=255)

                                                                                                 gATGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCGTGc                             >  2:433689/1‑139 (MQ=255)

                                                                                                   tGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGccc                                                                                               <  1:723096/71‑1 (MQ=255)

                                                                                                   tGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGccc                                                                                               >  2:723096/1‑71 (MQ=255)

                                                                                                   tGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCGTGCCg                           <  2:156072/139‑1 (MQ=255)

                                                                                                   tGGCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCGTGCCg                           <  2:551125/139‑1 (MQ=255)

                                                                                                     gCAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCGTGCCGTc                         <  1:622204/139‑1 (MQ=255)

                                                                                                      cAATTTTTGATATCCAGGAACTGAAGCAGGAAGCATAAAACTATCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCGTGCCGTcc                        >  1:278543/1‑139 (MQ=255)

                                                                                                               atatCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGccc                                                                                               >  2:265823/1‑59 (MQ=255)

                                                                                                               atatCCAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGccc                                                                                               <  1:265823/59‑1 (MQ=255)

                                                                                                                    cAGGAACTGAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCGTGCCGTCCAATTTGATATCGcc          <  1:290899/139‑1 (MQ=255)

                                                                                                                            gAAGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCGTGCCGTCCAATTTGATATCGCCAAACGGAt  <  2:123353/139‑1 (MQ=255)

                                                                                                                             aaGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCt                                                                     <  1:33534/71‑1 (MQ=255)

                                                                                                                             aaGCAGGAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCt                                                                     >  2:33534/1‑71 (MQ=255)

CCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGCTTCTCCCAAACCAAGGTTTTCGAGAGCCTTTTGCACCGTGCCGTCCAATTTGATATCGCCAAACGGAT  >  NC_000913/2471688‑2471950

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A