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
A5 F23 I1 R1	20	46.9	1668438	94.0%	1568331	143.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_hsa_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_hsa_tpiA	2,106,741	0	A	T	97.8%	150.7 / NA	46	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (26/19); minor base C (1/0); total (27/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTC  >  NC_000913_3_hsa_tpiA/2106603‑2106885

aaCACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaataa                                                                                                                                         >  1:42971/1‑149 (MQ=255)

      tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAg                                                                                                                                   <  1:116333/149‑1 (MQ=255)

         gATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaa                                                                                                                                >  1:823526/1‑149 (MQ=255)

               tGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagtag                                                                                                                          >  1:284373/1‑149 (MQ=255)

                 cATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAagacgtt                                                                                                                        >  1:185975/1‑144 (MQ=255)

                   tAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAg                                                                                                                      >  1:355519/1‑149 (MQ=255)

                         atgatAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTTGTTAGAATGAt                                                                                                                >  1:664701/1‑149 (MQ=255)

                          tgagAACCAAAAAGATAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACAGTGGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAtt                                                                                                               <  2:400002/149‑1 (MQ=255)

                            atAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                             >  2:98123/1‑149 (MQ=255)

                             tAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑c                                                                                                           <  2:284373/149‑1 (MQ=255)

                              aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑Ct                                                                                                          <  2:77448/149‑1 (MQ=255)

                              aaCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGAATGAGTAAATTTTTTTGACCACATAAATAAAGCAAAAGTAGTTAGAATGATTggtt                                                                                                           >  1:206694/1‑147 (MQ=255)

                              aaCAATAAAGACAATTTGGTGAGCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAACAAATAAATCAATAGTAGTTAGAATGATTGG‑Ct                                                                                                          <  2:77479/149‑1 (MQ=255)

                               aCCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACTAAATAAATAAAGCAAAAGTAGTTAGATTGATTGT‑CTg                                                                                                         >  2:334095/1‑149 (MQ=255)

                                 cATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCa                                                                                                       <  1:528391/149‑1 (MQ=255)

                                  aTAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCAt                                                                                                      <  2:339103/149‑1 (MQ=255)

                                  aTAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCAt                                                                                                      >  1:339103/1‑149 (MQ=255)

                                       actaaTTTGCTTACCAGGATTAAGCAAAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTATATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATg                                                                                                 <  1:409913/146‑1 (MQ=255)

                                                 ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCATATAAATAAAGCAAAATTAGTTAGAATGATTGA‑CTAAATGTATTATGAGAAGtt                                                                                       >  2:431310/1‑149 (MQ=255)

                                                 ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGTATGATTGG‑CTGCATGTATGCTGAGAAAtt                                                                                       >  1:732676/1‑149 (MQ=255)

                                                               tataATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCtt                                                                         >  1:345138/1‑149 (MQ=255)

                                                                ataATTGTAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTc                                                                        <  1:79146/149‑1 (MQ=255)

                                                                   aTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTCACTTTGGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAAc                                                                     <  1:444036/149‑1 (MQ=255)

                                                                     tGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACAt                                                                   >  2:446636/1‑149 (MQ=255)

                                                                       cAAAGATGAATACAATAAAAACAAGTAAAGCAAATGTTTTACTTACCTGGGTAATAGCAAATTTTTTCGACCAAATAAATAAAGCAAAAGTAGTGAGAATCATTTG‑CTGCATGTATGCTGAGAAATTTCTTGATGTATCTTCACCCTCa                                                                 >  2:32754/1‑149 (MQ=255)

                                                                            aTGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTTTTTTTTTTATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGTTTTCTCTTCAATATCCGCAtc                                                            >  2:273365/1‑149 (MQ=255)

                                                                                 taaaaTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTa                                                       <  1:340795/146‑1 (MQ=255)

                                                                                 tACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGCA‑GATGGGTCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTa                                                       >  1:404877/1‑149 (MQ=255)

                                                                                          aaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCa                                              >  1:465568/1‑149 (MQ=255)

                                                                                                   agtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGTATCTCTTATCAAATTCATATAGCtaa                                     <  1:242879/149‑1 (MQ=255)

                                                                                                   agtaaaTGTTGTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                     <  2:690308/149‑1 (MQ=255)

                                                                                                       aaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAACGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTTTTAAACATCAGCATATCTTATCAAATTCATATAGCtacttca                                 >  2:707346/1‑144 (MQ=255)

                                                                                                       aaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagtaa                                 >  1:344872/1‑149 (MQ=255)

                                                                                                       aaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagtaa                                 >  1:44684/1‑149 (MQ=255)

                                                                                                         tGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGc                               <  2:344872/149‑1 (MQ=255)

                                                                                                             ttacttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGt                           <  1:611213/149‑1 (MQ=255)

                                                                                                               acttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTcc                         <  1:371857/149‑1 (MQ=255)

                                                                                                               acttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGA‑CTGCATGTATGCTGAGAAATTTCTTGATGTGACTTCCGCATCAGCATCTCTTATCAAATTCATAGAGCTAATTAAGCTACTcc                         >  2:787992/1‑149 (MQ=255)

                                                                                                                 ttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTAAGAAATTTCTTGATGTGTCTTCAACATAAACATCTCTTATCAAATTCATATCGCTATGTATGTTAGTCCCg                       >  2:49304/1‑149 (MQ=255)

                                                                                                                    ccTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑c                                                                                                           >  1:728073/1‑62 (MQ=255)

                                                                                                                    ccTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑c                                                                                                           <  2:728073/62‑1 (MQ=255)

                                                                                                                     cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTAATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt                   >  2:693373/1‑149 (MQ=255)

                                                                                                                        tGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGt                <  2:413308/149‑1 (MQ=255)

                                                                                                                           aTTAGTAAATTTTTTTGCCCAAATAAATAAAGCAAAATTAGTTAGAATGATTGG‑CTGAATGTATGCTTAGCAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTCAGCTAGTCTCAACATGGTAGt             >  2:679995/1‑149 (MQ=255)

                                                                                                                                tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACtt        >  1:30654/1‑149 (MQ=255)

                                                                                                                                      ttttTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTc  <  1:749876/149‑1 (MQ=255)

AACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGG‑CTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCTC  >  NC_000913_3_hsa_tpiA/2106603‑2106885

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