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
A24 F21 I1 R1	17	36.5	1286766	92.7%	1192832	143.7

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	96.0%	151.0 / NA	51	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand): ref base A (2/0); new base T (23/25); total (26/25)
Fisher's exact test for biased strand distribution p-value = 4.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC  >  NC_000913_3_pae_tpiA/2106597‑2106882

tctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGAcc                                                                                                                                           >  1:629153/1‑149 (MQ=255)

   aTTAACACCTACGATGAATGCATAAGAGATGATAACTCTAAAGCCCCTTTGCTTACTAGTATACAGAATACTCGTCACGTTCATTATTACAGAAATAAGTAAAGGTAATTCTTTACTAACCTGGTTAGTAGTAAAATTTTTTGATCaaa                                                                                                                                        >  2:151898/1‑149 (MQ=255)

         acCTACGATGAATGCATAAGAGATGATAACCATAAAGAACATTTGCTTACCAGTATTCCGTATAAGTACAAATATGAATACAATAAAAACAAATAAAGTAAATGTTTTACTTACATTTGTATTAGTAAATTTTTTTAATCAaataaata                                                                                                                                  >  2:299200/1‑149 (MQ=255)

            tACGATAAATATATAAGTAATTGTAACCTTAAAGCAACTGTTGTTACCATTATTCACTATAATAGCAAATATGAATAAAATTATTACAAGCAAAGTAAAATTTTTACTTACCTTTGTATTAGTTAATTTTTTTGACAGATTAAATAAAg                                                                                                                               <  2:116897/149‑1 (MQ=255)

              cGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAGTTGCAAAGATGAATACAATCAAAACAAGTAAAGTCAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCa                                                                                                                             >  2:487237/1‑149 (MQ=255)

                aTGAAAGCATAAGAGATGATAACCATAAATACTATTTCATTAACAAAATAAAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTATCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaaa                                                                                                                           <  1:974/149‑1 (MQ=255)

                        aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAGCGGAAATGTTTTAACAACGATGGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTa                                                                                                                   >  1:284845/1‑149 (MQ=255)

                        aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAATAAAGGTTTTCATTCCACAATTATGAGTAAATTTTTTTTACCAAATAAATAAAGCAAAAGTAGTTa                                                                                                                   <  1:151898/149‑1 (MQ=255)

                            gaaaaaatAACCATAAATACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                               <  1:83674/143‑1 (MQ=255)

                                    aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCt                                                                                                       >  1:138341/1‑149 (MQ=255)

                                       cATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCa                                                                                                    <  1:629207/149‑1 (MQ=255)

                                        aTAAATACAATTTGCGTACTAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCAt                                                                                                   <  2:573226/149‑1 (MQ=255)

                                         tAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAATACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAATCAAAATTAGTTAGAATGATTTGCTCCATg                                                                                                  >  2:24965/1‑149 (MQ=255)

                                                aaTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGATTGATTGGCTGCATGTATGCTg                                                                                           >  2:289374/1‑149 (MQ=255)

                                                aaTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTg                                                                                           >  1:76812/1‑149 (MQ=255)

                                                 atgtGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTga                                                                                          <  2:122604/146‑1 (MQ=255)

                                                  tttGCTTATCAGTATGCAATATAATTACAAAGATGAATAAAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTgag                                                                                         <  2:600272/149‑1 (MQ=255)

                                                   ttGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                         >  2:505907/1‑132 (MQ=255)

                                                   ttGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                         <  1:505907/132‑1 (MQ=255)

                                                     gCTGACCAGTATTCACTTTAATTGCAAAGATGAATACAATAAATACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGaaa                                                                                      <  2:55733/149‑1 (MQ=255)

                                                       ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAACGTAAATGTTTTACTTACTTTTCTATTAGTATATTATTTAGATCAAAAAAATAAAGCAAAAGAAGTAAAAATGAATGGCTACATGTATGCTGAGAAAtt                                                                                    >  1:128213/1‑149 (MQ=255)

                                                       ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTCCACCAAAAATGGAAATCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAAtt                                                                                    >  2:458914/1‑149 (MQ=255)

                                                         aCCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTc                                                                                  >  1:35417/1‑149 (MQ=255)

                                                         aCCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATAATTGGCTGCATGTATGCTGAGAAATTTc                                                                                  >  2:616611/1‑149 (MQ=255)

                                                           cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATTAAACAAAAGTAGTTAGAATGATTGGCTGCATATATGCTGTGAACTTTCtt                                                                                >  2:403883/1‑149 (MQ=255)

                                                              tATGCATTATAATTGCAAAGTTGAATACAATAAACACAAGTAAAGTAAATGTTTTTCTTACCTTTGTATTAGTAAATTTATATGACCAAATAAATAAAGCAAAAGAAGTTAGAATTATTGGCTGCATGTATCCCGAGAAATTCCTTGAt                                                                             <  2:528407/149‑1 (MQ=255)

                                                                   aGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATCAATAAATCAAAAGTAGTTAGAATGATTGTCTGCATTTATTGTGATAAATTTCTTGAtgtttt                                                                        >  2:211101/1‑146 (MQ=255)

                                                                        aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa                                                                   <  1:371876/149‑1 (MQ=255)

                                                                        aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCCTCaa                                                                   <  1:48373/149‑1 (MQ=255)

                                                                         aatGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAAc                                                                  <  1:127469/147‑1 (MQ=255)

                                                                           tGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACAt                                                                >  1:490862/1‑149 (MQ=255)

                                                                           tGCAAAGATGAATAAAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCAGGTATGCTGAGAAATTTCTTGATGTGTCTTCAACAt                                                                <  2:461549/149‑1 (MQ=255)

                                                                                   tGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCAtct                                                        <  2:412505/149‑1 (MQ=255)

                                                                                                   aagtaaagtaAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAACGTAGATAGAATGATTGGCTGCATGTATGAAGAGAAATAGCGTTATGTGTCTTCAATATTAGCATCTCTTATCAAATTTatct                                        >  2:458699/1‑147 (MQ=255)

                                                                                                   aagtaaagtaAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCatat                                        >  1:509775/1‑149 (MQ=255)

                                                                                                    agtaaagtaaATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCAtata                                       <  2:284845/149‑1 (MQ=255)

                                                                                                      taaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGc                                     >  1:236094/1‑149 (MQ=255)

                                                                                                           taaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagt                                >  1:596769/1‑149 (MQ=255)

                                                                                                               tGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGAACTAATAATTAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc                            <  1:339434/149‑1 (MQ=255)

                                                                                                                       ttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCg                    >  1:412905/1‑149 (MQ=255)

                                                                                                                         acCTTTGTATTATTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGaa                  <  1:225135/149‑1 (MQ=255)

                                                                                                                           cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt                >  1:281017/1‑149 (MQ=255)

                                                                                                                            tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaag                                 >  1:283721/1‑131 (MQ=255)

                                                                                                                            tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaag                                 <  2:283721/131‑1 (MQ=255)

                                                                                                                            tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCTAACTg               >  2:228185/1‑149 (MQ=255)

                                                                                                                            tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg               <  2:412026/149‑1 (MQ=255)

                                                                                                                              tGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGt             <  1:487237/149‑1 (MQ=255)

                                                                                                                                tATTAGTAAATTTTTTTTACCAAAAAAACAAACAAAAAGAAGGTATAATGATTGGCTGCACGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAACTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAg           <  1:339431/149‑1 (MQ=255)

                                                                                                                                       aaaTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCCTATCACTTAGTAAGCTAGTCCCGAACTGGTAGTTACTTa    <  2:462149/149‑1 (MQ=255)

                                                                                                                                         aTTTTTTTTACCAAATAAATAAAGAAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATATCTTGATGTGTCTTCAAAATCAGCATCTCTTATTTAATTAATATAGCTAAGTAAGCTAGTCCCAAACTGGTTGTTACTTAAc  >  2:394784/1‑149 (MQ=255)

                                                                                                                                         aTTGTTTTGACCAAATAAATAAAGCAAAAGTAGTTTGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCATCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc  <  1:158105/149‑1 (MQ=255)

TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAC  >  NC_000913_3_pae_tpiA/2106597‑2106882

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