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 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,983,288	C→T	279 (TAG→TAA)	kduI ←	hexuronate isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,983,288	0	C	T	100.0%	103.6 / NA	34	279 (TAG→TAA)	kduI	hexuronate isomerase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (15/19); total (15/19)

AGCCCGCTTGCGCCAGCCCCAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAACTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCGGGGAGATCA  >  NC_000913/2983156‑2983415

aGCCCGCTTGCGCCAGCCCCAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAgcgc                                                                                                                           <  2:325231/139‑1 (MQ=255)

                   cAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACAt                                                                                                        <  1:743925/139‑1 (MQ=255)

                          aTCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCa                                                                                                  <  2:518425/138‑1 (MQ=255)

                          aTCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCa                                                                                                  >  1:518425/1‑138 (MQ=255)

                           tCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                         >  1:430067/1‑130 (MQ=255)

                           tCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                         <  2:430067/130‑1 (MQ=255)

                           tCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcac                                                                                                          <  2:366662/129‑1 (MQ=255)

                           tCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcac                                                                                                          >  1:366662/1‑129 (MQ=255)

                           gagatagACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTTACGGCCACATGGTCCata                                                                                                <  1:612752/133‑1 (MQ=255)

                                tGACCCAGT‑CAATATTAAAACCAATGGCCGCCCCAACCTTAACTTCCGGAGAAAAAGCACCTTAAATCATTACCAAACCTTATTCGTTTAATCCCACCATTAGCGCAAATCTTTAACGGCCACATGGTCCATAtcatca                                                                                          <  2:893781/139‑1 (MQ=255)

                                 gACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATAtcatca                                                                                          <  2:31511/139‑1 (MQ=255)

                                             tATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAACCATAACAATACCTTATTCGTTTATGCCCAAAATTAGCGCAAATCTTTAACGGCCACATGGACCATATCATCAAAGACCTgtctc                                                                              >  2:612752/1‑135 (MQ=255)

                                                  caACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                         <  2:444762/107‑1 (MQ=255)

                                                  caACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                         >  1:444762/1‑107 (MQ=255)

                                                  caACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCAcc                                                                         >  1:557673/1‑139 (MQ=255)

                                                        gTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCAt                                                                   >  1:678773/1‑139 (MQ=255)

                                                           acgacCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGcc                                                                <  2:122881/139‑1 (MQ=255)

                                                             gacCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCatat                                                                                               >  2:904030/1‑106 (MQ=255)

                                                             gacCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCatat                                                                                               <  1:904030/106‑1 (MQ=255)

                                                              acCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACgg                                                                                                              >  1:719295/1‑90 (MQ=255)

                                                              acCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACgg                                                                                                              <  2:719295/90‑1 (MQ=255)

                                                                               gagagaAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                         <  2:104638/78‑1 (MQ=255)

                                                                               gagagaAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                         >  1:104638/1‑78 (MQ=255)

                                                                                agagaAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcac                                                                                                          <  1:850760/76‑1 (MQ=255)

                                                                                agagaAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcac                                                                                                          >  2:850760/1‑76 (MQ=255)

                                                                                agagaAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCttt                                           >  2:352065/1‑139 (MQ=255)

                                                                                          cACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTCACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGaca                                 <  2:580054/139‑1 (MQ=255)

                                                                                               aaaaTCATAACAATACCTTATTCGTTTATGTCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGa                            <  1:352065/139‑1 (MQ=255)

                                                                                                                 tATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                         <  2:149779/44‑1 (MQ=255)

                                                                                                                 tATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                         >  1:149779/1‑44 (MQ=255)

                                                                                                                   ttCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCgggg        <  2:557673/139‑1 (MQ=255)

                                                                                                                        ttATGCCCACAATTAGCGCAAATCTTTAGCGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGAcc                                                                     <  1:682399/73‑1 (MQ=255)

                                                                                                                        ttATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGCCCTGGTTTTCACCGAcc                                                                     >  2:682399/1‑73 (MQ=255)

                                                                                                                         tATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCGGGGAGATCa  >  1:489625/1‑139 (MQ=255)

AGCCCGCTTGCGCCAGCCCCAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAACTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCGGGGAGATCA  >  NC_000913/2983156‑2983415

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A