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
A8 F9 I0 R1	23	38.9	1378630	88.6%	1221466	148.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	2,106,741	A→T	100%	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	100.0%	99.6 / NA	30	S162S (TCT→TCA)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (16/14); total (16/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCT  >  NC_000913_3_hsa_tpiA/2106606‑2106884

acCTACGATTAATGTATATGAGTTGATAACCATAATGACAATTTGCTTAACAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAaataaata                                                                                                                                    <  1:49666/149‑1 (MQ=255)

acCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTTAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAaataaata                                                                                                                                    <  1:49489/149‑1 (MQ=255)

  cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAATAATCAGTATAATTGCACAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                  >  1:650069/1‑149 (MQ=255)

              cATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGATTATATAAATAAACCAAAAGTAGtt                                                                                                                      >  2:530682/1‑149 (MQ=255)

               aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTa                                                                                                                     >  1:164364/1‑149 (MQ=255)

               aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTCTGTATTAGTAAATTTATTTGACCACATAAATAAAGAAAAAGTAGttc                                                                                                                     >  2:156389/1‑148 (MQ=255)

                 aaGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAATTAAAGCAAAAATAGTTAGa                                                                                                                   >  2:222666/1‑149 (MQ=255)

                      aggatAAACATTAAGACAATTTGCTTACCAGTATTAAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAt                                                                                                              <  2:41324/147‑1 (MQ=255)

                       tgatAACCATAAAGACCATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAtt                                                                                                             <  1:528680/149‑1 (MQ=255)

                               attaaGAAAATTGGCGTACCAGGATTGAGGATAATTGCAAAGATGAATACAAGAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCAt                                                                                                     <  2:108743/146‑1 (MQ=255)

                               aTAAAGACAAATTGCTTACCAGTAGTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCAt                                                                                                     <  1:298762/149‑1 (MQ=255)

                                   aGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTTCATGTAt                                                                                                 >  2:464811/1‑149 (MQ=255)

                                    gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATg                                                                                                >  2:680121/1‑149 (MQ=255)

                                       aaTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGACTGCATGTATGCTg                                                                                             >  1:141554/1‑149 (MQ=255)

                                              ctaacAGTATTAAATATAATTGCAAAGATGAATACAATAAAAACCAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAAtt                                                                                      <  2:543911/145‑1 (MQ=255)

                                                     tATTCAGTATAATAGTAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTAGTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                               <  2:122311/149‑1 (MQ=255)

                                                         aaGTAAAAATGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATgtgt                                                                           <  1:371091/148‑1 (MQ=255)

                                                          aGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTACTAAATTAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTTAGAAATTTCTTGCTGTGTc                                                                          >  2:398371/1‑149 (MQ=255)

                                                               aaTTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCaa                                                                     <  1:415906/149‑1 (MQ=255)

                                                                         aTGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGCTTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTATTCTACATCAGCAtc                                                           >  1:427889/1‑149 (MQ=255)

                                                                         aTGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCGGCATGTATGCTGAGAAATTTCTTGATGTGTTTTCAACATCAGCAtc                                                           >  1:618676/1‑149 (MQ=255)

                                                                                   tAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaaa                                                 >  1:496898/1‑149 (MQ=255)

                                                                                   tAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaaa                                                 <  1:180166/149‑1 (MQ=255)

                                                                                   tAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGAATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCaac                                                 >  1:403981/1‑148 (MQ=255)

                                                                                      aaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTc                                              >  1:399850/1‑149 (MQ=255)

                                                                                             taaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGc                                       <  1:540503/149‑1 (MQ=255)

                                                                                                agtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTAATGTGTCTTCAACATCAACATCTCTTATCAAATTAATATAGCtaa                                    >  1:9918/1‑149 (MQ=255)

                                                                                                                          aaGTAAATTTTTTTGACCAAATAAATAAAGAACAAGTCGTTCGTCTGCTTGGCTGCTCGCAACCTGAGAAATTTCATGATGTGTCTGGTAGGTCTGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTa          <  2:661579/148‑1 (MQ=255)

                                                                                                                             tAAATTTTTTTGACCAAATAAATAAGGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATATCTTGATGTGTCTTCAACATCAGCATCTCTTATCGAATTCATATAGCTAAGTAAGCTAGTCCCGAGCTGGTAGTTACtt       >  1:520423/1‑149 (MQ=255)

                                                                                                                                aTTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAc    <  2:609875/149‑1 (MQ=255)

                                                                                                                                  ttttttGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGACTCGAGGGATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCt  <  1:673492/149‑1 (MQ=255)

ACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACCT  >  NC_000913_3_hsa_tpiA/2106606‑2106884

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