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
A15 F3 I1 R1	17	41.7	1441332	93.3%	1344762	144.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	2,106,741	A→T	S162S (TCT→TCA)	wbbH ←	O‑antigen polymerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	2,106,741	0	A	T	100.0%	96.4 / NA	31	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (18/13); total (18/13)

TATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACT  >  NC_000913_3_pae_tpiA/2106599‑2106868

tATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaa                                                                                                                           >  1:269243/1‑149 (MQ=255)

    aaCACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAAAAAGTAAAGTAAATGTTTTCATTACACTTGTATTAGTAAATTTTTTTGACCaaataa                                                                                                                       >  2:667822/1‑149 (MQ=255)

          tACAATGGATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTATTTACCTTTTTATTAGTAAATTTTTTTGACCAAATAAATAAAg                                                                                                                 <  2:519135/149‑1 (MQ=255)

             gATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaa                                                                                                              >  1:660709/1‑149 (MQ=255)

               agacagCAGAAGAGATGATAACCATAAAGACTATATGCTTACCACTATTCAGTAAAATTAAAAAAAAGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAaaaaaaaaaaaaaaaa                                                                                                            <  2:656639/144‑1 (MQ=255)

                      aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTa                                                                                                     >  2:66008/1‑149 (MQ=255)

                              tgatAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAtt                                                                                             <  2:269243/149‑1 (MQ=255)

                                  aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCt                                                                                         >  2:76720/1‑149 (MQ=255)

                                          aGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTAt                                                                                 <  2:660709/149‑1 (MQ=255)

                                            aCAATTTGATTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGc                                                                               <  2:615930/149‑1 (MQ=255)

                                                              ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                             >  1:603324/1‑149 (MQ=255)

                                                                      aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa                                                     <  2:385885/149‑1 (MQ=255)

                                                                           cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                <  2:417137/149‑1 (MQ=255)

                                                                           cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATATTTTTGAACAAATAAATAAAGCAAACGTAGTTAGAATGATTGCCTGCATGTATGCTGAGAAATTTCTTGATGTGTATTCAACATcc                                                >  2:462169/1‑148 (MQ=255)

                                                                            aaaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAg                                               <  1:452074/149‑1 (MQ=255)

                                                                              aGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCTGCa                                             >  1:190043/1‑149 (MQ=255)

                                                                              aGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATATTTGGCATTGATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCa                                             >  1:421121/1‑149 (MQ=255)

                                                                                      aCAATCAAAACAACAAAAGTAAATTGTTTACTTACCTTTGCATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTAt                                     <  2:216258/149‑1 (MQ=255)

                                                                                         aTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaa                                  >  1:513116/1‑149 (MQ=255)

                                                                                             aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                              >  1:306194/1‑149 (MQ=255)

                                                                                             aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                              <  1:76720/149‑1 (MQ=255)

                                                                                             aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTCATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                              <  1:66008/149‑1 (MQ=255)

                                                                                                cAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCata                           <  1:367101/149‑1 (MQ=255)

                                                                                                   gtaaagtaaaTGTTTTACTTACATTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCATAAGTAGTTAGAATGATTTGCTGCATGTATGCTGAGAAATTTTTTGATGTATATTTAACATTAGCATATCGTATCAAATTCattttc                        >  2:347669/1‑145 (MQ=255)

                                                                                                    taaagtaaaTGTTTTACTTACCTAAGTATTAGTAAATTTTTTTGAACAAATAAATTAACCAAAAGCAGTAAGAATGATTGGCTGCATGTATGCAGAGAAGTTTATTGATATATCTTCATATGAAGCATACCTTTTCACATTCATATAga                       >  2:116916/1‑148 (MQ=255)

                                                                                                     aaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCt                      >  1:34253/1‑149 (MQ=255)

                                                                                                        gtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaag                   >  1:558922/1‑149 (MQ=255)

                                                                                                         taaaTGTTTTACATACCTTTGTAGAAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATACCtaagt                  >  2:431487/1‑149 (MQ=255)

                                                                                                               ttttACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTa            >  1:520921/1‑149 (MQ=255)

                                                                                                                 ttacttaaCTTTGGATTAGTAAATTTTTTTGAGCAAATAAATAAAGAAAAAGTAGTTAGAATGATTGGCTGTATGTATGCTGAGAAATTTCTTTATTTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAGGTAAGCTAGt          <  2:283925/149‑1 (MQ=255)

                                                                                                                         cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt  >  1:191220/1‑149 (MQ=255)

TATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACT  >  NC_000913_3_pae_tpiA/2106599‑2106868

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A