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
A11 F1 I1 R1	63	64.8	2934156	93.7%	2749304	111.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,232,207	T→C	S181S (AGT→AGC)	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,232,207	0	T	C	100.0%	142.5 / NA	38	S181S (AGT→AGC)	fadH	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (16/22); total (16/22)

TCCTGCAACTGATCGACAATTTCGCCCGCTGCGCGCAACTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGTGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCATTATTATCTACCGACTGTCGATGCTCGACCTGGTCGAAGA  >  NC_000913/3232074‑3232335

tgcTGCAACTGATCGACAATTTCGCCCGCTGCGCGCAACTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCa                                                                                                                             >  2:880346/3‑139 (MQ=255)

 ccTGCAACTGATCGACAATTTCGCCCGCTGCGCGCAACTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAg                                                                                                                            <  2:98953/139‑1 (MQ=255)

     cAACTGATCGACAATTTCGCCCGCTGCGCGCAACTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTggg                                                                                                                        <  2:680634/139‑1 (MQ=255)

           aTCGACAATTTCGCCCGCTGCGCGCAACTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGgcggcg                                                                                                                  >  1:1114125/1‑139 (MQ=255)

           aTCGACAATTTCGCCCGCTGCGCGCAACTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGgcggcg                                                                                                                  >  1:193867/1‑139 (MQ=255)

           aTCGACAATTTCGCCCGCTGCGCGCAACTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGgcggcg                                                                                                                  >  1:1172837/1‑139 (MQ=255)

                   tttCGCCCGCTGCGCGCAACTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGc                                                                                                          <  2:1213626/139‑1 (MQ=255)

                      cGCCCGCTGCGCGCAACTGGCGCGGGAGACAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAAc                                                                                                       <  1:880346/139‑1 (MQ=255)

                              gcgcgcAACTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCg                                                                                               >  1:1197578/1‑139 (MQ=255)

                                    aaCTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGc                                                                                         <  2:38923/139‑1 (MQ=255)

                                    aaCTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGc                                                                                         <  2:1114125/139‑1 (MQ=255)

                                      cTGGCGCGGGAGGCAGGATACGACTGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCg                                                                                       <  1:820772/139‑1 (MQ=255)

                                      cTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCg                                                                                       <  1:1106998/139‑1 (MQ=255)

                                      cTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCg                                                                                       <  2:1255266/139‑1 (MQ=255)

                                                     ggATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAgtgcgtg                                                                        <  1:405451/139‑1 (MQ=255)

                                                                tgtAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGaa                                                             >  1:787174/1‑139 (MQ=255)

                                                                 gtAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAAc                                                            <  1:870071/139‑1 (MQ=255)

                                                                          aTGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGAtt                                                                                            <  2:176445/98‑1 (MQ=255)

                                                                          aTGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGAtt                                                                                            >  1:176445/1‑98 (MQ=255)

                                                                          aTGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCa                                                   >  2:236837/1‑139 (MQ=255)

                                                                            gggTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAAc                                                 <  2:807349/139‑1 (MQ=255)

                                                                               ttCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGAc                                              <  2:193867/139‑1 (MQ=255)

                                                                                   gAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCa                                          <  2:1197578/139‑1 (MQ=255)

                                                                                                 cAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGAttt                                                                                           >  2:893517/1‑76 (MQ=255)

                                                                                                 cAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGAttt                                                                                           <  1:893517/76‑1 (MQ=255)

                                                                                                 cAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCa                                          <  1:78051/125‑1 (MQ=255)

                                                                                                 cAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCa                                          >  2:78051/1‑125 (MQ=255)

                                                                                                 cAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCATTATTATCTACCGa                            >  2:897117/1‑139 (MQ=255)

                                                                                                   aCGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGgcggcg                                                                                                                  >  1:468501/1‑51 (MQ=255)

                                                                                                   aCGAATTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGgcggcg                                                                                                                  <  2:468501/51‑1 (MQ=255)

                                                                                                      aaTTTCTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCATTATTATCTACCGACTGTc                       <  1:897117/139‑1 (MQ=255)

                                                                                                           cTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGAt                                                                                             >  2:1223179/1‑64 (MQ=255)

                                                                                                           cTGACGCTGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGAt                                                                                             <  1:1223179/64‑1 (MQ=255)

                                                                                                                  tGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCATTATTATCTACCGACTGTCGATGCTCGACCt           >  2:820000/1‑139 (MQ=255)

                                                                                                                  tGCGCACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCATTATTATCTACCGACTGTCGATGCTCGACCt           >  2:953310/1‑139 (MQ=255)

                                                                                                                    cgcACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCATTATTATCTACCGACTGTc                       >  2:325346/1‑125 (MQ=255)

                                                                                                                    cgcACCAATCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCATTATTATCTACCGACTGTc                       <  1:325346/125‑1 (MQ=255)

                                                                                                                           aTCAGCGTAGCGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCATTATTATCTACCGACTGTCGATGCTCGACCTGGTCGAAGa  <  2:1172837/139‑1 (MQ=255)

TCCTGCAACTGATCGACAATTTCGCCCGCTGCGCGCAACTGGCGCGGGAGGCAGGATACGACGGTGTAGAGGTGATGGGTTCCGAAGGGTATTTGATCAACGAATTTCTGACGCTGCGCACCAATCAGCGTAGTGACCAGTGGGGCGGCGATTACCGCAACCGGATGCGATTTGCCGTAGAAGTAGTGCGTGCGGTGCGCGAACGCGTCGGCAACGACTTCATTATTATCTACCGACTGTCGATGCTCGACCTGGTCGAAGA  >  NC_000913/3232074‑3232335

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A