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
A0 F0 I1 R1	16	48.9	1703346	91.6%	1560264	146.2

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%	137.1 / NA	46	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (21/25); total (21/25)

TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCT  >  NC_000913_3_pae_tpiA/2106597‑2106884

tctATTAACACCTACGATGAATGCATAAGAGATGATAACCATACAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTCACCACTCTCGTTTTAGTAAATTTTTTTGAcc                                                                                                                                             >  2:173520/1‑149 (MQ=255)

 ctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTACCa                                                                                                                                            >  1:74546/1‑149 (MQ=255)

   aTTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaa                                                                                                                                          <  2:750675/149‑1 (MQ=255)

    ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaat                                                                                                                                         >  2:213736/1‑149 (MQ=255)

    ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaat                                                                                                                                         >  1:578092/1‑149 (MQ=255)

       acacCGACGATGAATGCATAGGATATAATAACCATAAAGACAATTTGCTTACCATTATTCAGTATAATGGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaataaa                                                                                                                                      <  1:173520/149‑1 (MQ=255)

          ccTACGATGAATGCATAAGAGATGATAAACATAAAGACAATTGGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAGAGTAAATGTTTTACTTAACTTTGTATTAGTAAATTTTTTTGATCAAataaataa                                                                                                                                   >  2:14488/1‑149 (MQ=255)

           cTACGATGAATGCATAAGAGATGATAACCACAAAGACAATTTGCTTACCAATATTCAGAATCATTGCAAAACTAAATACAACACCAACAAGTAAAGTAAAGGTTTTACTTACCATTGCATTAGTCAACTTCTTTCACCAagtaattaca                                                                                                                                  >  2:24583/1‑147 (MQ=255)

            tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAg                                                                                                                                 <  1:580372/149‑1 (MQ=255)

               gATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTGTAATTGCAAAGATGAATACAATACAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCACATAATTAAGGCaa                                                                                                                              >  1:241804/1‑149 (MQ=255)

                 tGAATGGATTAGAAATGATAACCATAAAGAAAATATGCTTATCAGTATTCATTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTGTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaaaa                                                                                                                            <  2:704490/149‑1 (MQ=255)

                      acATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtagt                                                                                                                       <  2:553852/148‑1 (MQ=255)

                         tAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTACCAAATAAATAAAGCAAAAGTAGTTAg                                                                                                                    >  2:738195/1‑149 (MQ=255)

                          aaGAGATGATAACCAGAAAGACAATATGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGa                                                                                                                   <  1:347669/149‑1 (MQ=255)

                            gagaTGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                                 <  1:26358/149‑1 (MQ=255)

                            gagaTGATAACCATAAAGACAATGTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                                 <  1:188060/149‑1 (MQ=255)

                                   tatcattAAATACGATTTGTTTAGCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGc                                                                                                          <  2:421767/143‑1 (MQ=255)

                                    aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCt                                                                                                         <  2:578092/149‑1 (MQ=255)

                                             gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATg                                                                                                >  1:649551/1‑149 (MQ=255)

                                             gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATAGGCTGCATGTATg                                                                                                >  2:598302/1‑149 (MQ=255)

                                               cAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCt                                                                                              <  2:777618/149‑1 (MQ=255)

                                                 aTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCCTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAATAGTTAGAATGATTGCCTGCATGTATGCTga                                                                                            >  2:116507/1‑149 (MQ=255)

                                                     gCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGaaa                                                                                        >  2:850183/1‑149 (MQ=255)

                                                           cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                  <  2:428415/149‑1 (MQ=255)

                                                           cAGTAATCAGTATAATTTCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                  <  1:645825/149‑1 (MQ=255)

                                                              tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                               >  1:508957/1‑149 (MQ=255)

                                                              tATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                               >  1:365331/1‑149 (MQ=255)

                                                                ttCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                             >  1:114784/1‑149 (MQ=255)

                                                                   aGTATAATTATATAGATATATACAATAAAAGATAGTAAAGTAATTGGTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTTGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc                                                                          <  2:194433/149‑1 (MQ=255)

                                                                         aTTGCAAAGATGAATAAAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTGAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAAc                                                                    <  2:74546/149‑1 (MQ=255)

                                                                          ttGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACa                                                                   >  1:650097/1‑149 (MQ=255)

                                                                           tGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTATTGATGTGTCTTCAACAt                                                                  >  1:131934/1‑149 (MQ=255)

                                                                             cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCa                                                                >  2:791150/1‑149 (MQ=255)

                                                                               aaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGc                                                              <  1:213736/149‑1 (MQ=255)

                                                                                           aTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaa                                                  >  1:569982/1‑149 (MQ=255)

                                                                                                     gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAg                                        <  1:605765/149‑1 (MQ=255)

                                                                                                     gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAg                                        >  1:595372/1‑149 (MQ=255)

                                                                                                        aagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCta                                     >  2:322081/1‑149 (MQ=255)

                                                                                                         agtacaTGTTTTAATTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                    <  1:830125/149‑1 (MQ=255)

                                                                                                         agtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                    <  1:322081/149‑1 (MQ=255)

                                                                                                               tGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc                              <  1:151297/149‑1 (MQ=255)

                                                                                                                gTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCt                             <  2:649551/149‑1 (MQ=255)

                                                                                                                            tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg                 <  1:287987/149‑1 (MQ=255)

                                                                                                                                    aGTAAATTTTTTTGACCAAATAAATAAAACAAAAATAATTATAATTATTTGCTGCATGTATGCTGATAAATTTCTTTATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTAc         <  2:44581/149‑1 (MQ=255)

                                                                                                                                        aaTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTaa     <  1:248413/149‑1 (MQ=255)

                                                                                                                                         aTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc    <  2:724848/149‑1 (MQ=255)

                                                                                                                                           ttttttGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATATCTAAGTAAGCTAGTCCCGAACTGGTAGTTATTTAACCt  >  2:744934/1‑149 (MQ=255)

TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCT  >  NC_000913_3_pae_tpiA/2106597‑2106884

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