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
A4 F6 I0 R1	31	40.7	1457906	90.0%	1312115	147.3

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	95.2%	128.9 / 0.1	42	coding (486/1167 nt)	wbbH	O‑antigen polymerase
Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (24/16); minor base . (1/1); total (25/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

ACTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACT  >  NC_000913_3_hsa_tpiA/2106595‑2106878

aCTATATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTAGTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGa                                                                                                                                         <  2:566448/149‑1 (MQ=255)

  tctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTCTTAGTCAATTTTTTTGAcc                                                                                                                                       >  1:303955/1‑149 (MQ=255)

  tctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTT‑GACCa                                                                                                                                      >  2:107390/1‑149 (MQ=255)

     aTTAACACCTACGATGAATGCATAAGATATGAGAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaa                                                                                                                                    <  2:382842/149‑1 (MQ=255)

      ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTACCaaat                                                                                                                                   >  2:511474/1‑149 (MQ=255)

             cTACGATGAATGCATAAGAGATGATCACCATAAAAACAATTTGCTTACCAGTATTGAGTATAAATGCATCGATGAATGCAATAAAAACAATAAAAGTAAAAATTTTATATATCTTGGTATTATTAAATGTTTTTAATAAATtaaataaa                                                                                                                            >  2:169195/1‑149 (MQ=255)

              tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAg                                                                                                                           >  2:497559/1‑149 (MQ=255)

                  aTGAATGCGTAAGATATGATAACCAGATAGACAAGTTGCTCACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTCACGTAAATGTTTTACTTACTTTTGTACTAGTAAATTTTTGTGACTTATTAAGTAAAGCaaa                                                                                                                       <  2:247987/149‑1 (MQ=255)

                          aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTGGTATTAGTAAATTTTTTTGCCTCAATAAATAAAGAAAAagtcgtga                                                                                                               >  1:495312/1‑147 (MQ=255)

                             agagATGATAACCATAAAGACAATTTGCTTACCAGTAGTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAATAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGaa                                                                                                            <  2:69926/149‑1 (MQ=255)

                                 atgatAAACAATAAGACAATTTGCTTAACAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGAAAAAGTAGTTAGAATGAt                                                                                                        <  2:274448/149‑1 (MQ=255)

                                   gatAACCATAAGGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTg                                                                                                      >  1:400459/1‑149 (MQ=255)

                                      aaCCATAAAGACAATTTGCCTACCAGTATTCCGTACAATCGCAAACATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCt                                                                                                   <  1:245187/149‑1 (MQ=255)

                                        ccATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTGAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATTAATAAAGCAAAAGTAGTTACAATAATTTTCTGc                                                                                                 >  2:630218/1‑149 (MQ=255)

                                          aTAAAGACACTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTCAATGTTTTAATTACCTTTGTATTAGTAAATGTTTTTCTTCAAATAAATAAAGCAAAACTAGATAGAATAATTAGCTGCAt                                                                                               >  2:60215/1‑149 (MQ=255)

                                                     ttGCTTAACAGTAGTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTgaga                                                                                    <  2:297169/149‑1 (MQ=255)

                                                         ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAAtt                                                                                >  1:580627/1‑149 (MQ=255)

                                                         ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGAATGCTgcagaatt                                                                                >  1:599412/1‑142 (MQ=255)

                                                           aCCAGTATTCAGTATAATTGCAAAGATAAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTc                                                                              <  1:490317/149‑1 (MQ=255)

                                                            ccAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTTTTTTTTTAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAGTTTCt                                                                             >  2:691846/1‑149 (MQ=255)

                                                             cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                            >  1:411881/1‑149 (MQ=255)

                                                             cAGTAATCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                            <  1:301280/149‑1 (MQ=255)

                                                                tATTTAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                         <  2:333251/149‑1 (MQ=255)

                                                                       tataATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTGGAagtggcgt                                                                  >  2:512740/1‑145 (MQ=255)

                                                                                aaaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAACGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAAATTCTTGATGTGTCTTCAACATCaa                                                         >  2:101507/1‑148 (MQ=255)

                                                                                aaaGATGAATACAATAAAAACAAGTAAAGTAAATGGTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAg                                                         <  2:309848/149‑1 (MQ=255)

                                                                                        aTACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATGAGTAAATTTTTTTGACCCCATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATctctg                                                 >  1:137863/1‑148 (MQ=255)

                                                                                         tACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTa                                                >  1:612429/1‑149 (MQ=255)

                                                                                         tACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTT‑GACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTAt                                               <  1:107390/149‑1 (MQ=255)

                                                                                           cAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATc                                              <  1:490852/149‑1 (MQ=255)

                                                                                                     aagtaaagtaAATGTTTTACTTCCCTTTGTATTAGTAAATTTTTTTTAATAAATAAATACAGGAAAAATAGTTAGATTGATTCACTTCATGTATGCTTAGGAATTTCTTGATGTGTCTTCAACATCTGCATCCCTTATCAAATTCatat                                    >  2:60896/1‑149 (MQ=255)

                                                                                                      agtaaagtaaATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGTGAAATGTCGTGTTATGTCTTCAACATACACATCCCTCATCACATTCatatc                                   >  2:499636/1‑148 (MQ=255)

                                                                                                       gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAg                                  >  2:92372/1‑149 (MQ=255)

                                                                                                           agtaaaTGTTATACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCAGGGATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                              <  1:202911/149‑1 (MQ=255)

                                                                                                                             cTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACt            >  2:28761/1‑149 (MQ=255)

                                                                                                                              tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg           <  1:92372/149‑1 (MQ=255)

                                                                                                                              tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg           >  1:320870/1‑149 (MQ=255)

                                                                                                                                  tATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAg       >  1:550347/1‑149 (MQ=255)

                                                                                                                                    ttAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGtt     <  1:508891/149‑1 (MQ=255)

                                                                                                                                    ttAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGtt     >  1:396150/1‑149 (MQ=255)

                                                                                                                                      aGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTAc   <  2:345734/149‑1 (MQ=255)

                                                                                                                                       gTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCACTTATCAAATTCATATATCTCAGTAAGCTGGTCCCGAGCTGGTAGTTACt  >  2:75748/1‑149 (MQ=255)

ACTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACT  >  NC_000913_3_hsa_tpiA/2106595‑2106878

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