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	2,034,536	G→A	pseudogene (486/663 nt)	yedS →	pseudogene, outer membrane protein homology, putative outer membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,034,536	0	G	A	100.0%	189.4 / NA	58	pseudogene (486/663 nt)	yedS	pseudogene, outer membrane protein homology, putative outer membrane protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (30/28); total (30/28)

AGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAGGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATG  >  NC_000913/2034416‑2034665

aGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActtt                                                                                                                 >  2:551006/1‑139 (MQ=255)

  aaGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                               <  2:8678/139‑1 (MQ=255)

         gACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCaa                                                                                                        >  1:121302/1‑139 (MQ=255)

              atatGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAAct                                                                                                                   <  2:366320/123‑1 (MQ=255)

              atatGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAAct                                                                                                                   >  1:366320/1‑123 (MQ=255)

               tatGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAg                                                                                                  >  1:271146/1‑139 (MQ=255)

                  gctgcCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGt                                                                                               <  2:113589/139‑1 (MQ=255)

                  gctgcCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGt                                                                                               <  1:551006/139‑1 (MQ=255)

                     gcCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGtaat                                                                                            <  2:303532/139‑1 (MQ=255)

                                gtggCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAgtgg                                                                                 >  1:581182/1‑139 (MQ=255)

                                        aCCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCAt                                                                         <  2:434726/139‑1 (MQ=255)

                                         ccTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCAtt                                                                        <  2:581182/139‑1 (MQ=255)

                                             tGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACTATTCggg                                                                    >  2:207733/1‑139 (MQ=255)

                                             tGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCggg                                                                    >  1:1043861/1‑139 (MQ=255)

                                              gCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGc                                                                   >  1:1020362/1‑139 (MQ=255)

                                                  gcgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                               >  1:370327/1‑91 (MQ=255)

                                                  gcgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                               <  2:370327/91‑1 (MQ=255)

                                                  gcgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCAtt                                                                        >  1:999525/1‑130 (MQ=255)

                                                  gcgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCAtt                                                                        <  2:999525/130‑1 (MQ=255)

                                                  gcgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGa                                                               >  2:299829/1‑139 (MQ=255)

                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGGTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGaa                                                              >  1:809641/1‑139 (MQ=255)

                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGaa                                                              <  1:473952/139‑1 (MQ=255)

                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGaa                                                              <  1:207733/139‑1 (MQ=255)

                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGaa                                                              <  2:809641/139‑1 (MQ=255)

                                                   cgcCGACAACTTCATGAACGGTCGTACTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGaa                                                              <  1:718203/139‑1 (MQ=255)

                                                    gcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGc                                                                                                                          <  1:381290/78‑1 (MQ=255)

                                                    gcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGc                                                                                                                          >  2:381290/1‑78 (MQ=255)

                                                           aCTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCgg                                                      <  2:1020362/139‑1 (MQ=255)

                                                             ttCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTa                                                    <  2:121302/139‑1 (MQ=255)

                                                                        tCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAAct                                                                                                                   >  2:810793/1‑65 (MQ=255)

                                                                        tCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAAct                                                                                                                   <  1:810793/65‑1 (MQ=255)

                                                                         cGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                               <  2:540797/52‑1 (MQ=255)

                                                                         cGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                               >  1:540797/1‑52 (MQ=255)

                                                                                aTGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCt                                 >  1:1031056/1‑139 (MQ=255)

                                                                                  ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGt                                      >  1:358829/1‑132 (MQ=255)

                                                                                  ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGt                                      <  2:358829/132‑1 (MQ=255)

                                                                                     gtTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgct                                                                                                              <  1:378175/57‑1 (MQ=255)

                                                                                     gtTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgct                                                                                                              >  2:378175/1‑57 (MQ=255)

                                                                                      ttGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCa                                                                                                   <  1:845087/67‑1 (MQ=255)

                                                                                      ttGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCa                                                                                                   >  2:845087/1‑67 (MQ=255)

                                                                                             cTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                     >  2:28052/1‑58 (MQ=255)

                                                                                             cTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                     <  1:28052/58‑1 (MQ=255)

                                                                                                   tAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                     <  1:971028/52‑1 (MQ=255)

                                                                                                   tAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                     >  2:971028/1‑52 (MQ=255)

                                                                                                    aaCAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATg             >  2:759253/1‑139 (MQ=255)

                                                                                                      cAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGACGGTTCCGGTTGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGt           <  2:685118/139‑1 (MQ=255)

                                                                                                      cAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGa               >  1:761734/1‑135 (MQ=255)

                                                                                                      cAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGa               <  2:761734/135‑1 (MQ=255)

                                                                                                      cAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGt           >  1:897259/1‑139 (MQ=255)

                                                                                                        aTGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGttt         >  1:203116/1‑139 (MQ=255)

                                                                                                          ggCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCg       >  2:881589/1‑139 (MQ=255)

                                                                                                           gCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCgg      >  2:430290/1‑139 (MQ=255)

                                                                                                            cttcttTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGt     <  2:271146/139‑1 (MQ=255)

                                                                                                              tcttTGGTTAAGTCGATGGCTTGAActttgctttg                                                                                                           >  2:20082/1‑35 (MQ=255)

                                                                                                              tcttTGGTTAAGTCGATGGCTTGAActttgctttg                                                                                                           <  1:20082/35‑1 (MQ=255)

                                                                                                               cttTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATg  >  2:82736/1‑139 (MQ=255)

                                                                                                                 ttGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTa    <  1:298994/135‑1 (MQ=255)

                                                                                                                 ttGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTa    >  2:298994/1‑135 (MQ=255)

AGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAGGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATG  >  NC_000913/2034416‑2034665

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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