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
A17 F48 I1 R1	90	35.3	1199032	98.5%	1181046	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	391,777	G→T	L277I (CTC→ATC)	insF‑2 ←	IS3 element protein InsF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	391,777	0	G	T	100.0%	101.6 / NA	31	L277I (CTC→ATC)	insF‑2	IS3 element protein InsF
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (20/11); total (20/11)

GATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCC  >  NC_000913/391643‑391845

gATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATgccgc                                                                 >  2:214273/1‑140 (MQ=255)

 atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATgccgcc                                                                >  1:152536/1‑140 (MQ=255)

 atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATgccgcc                                                                >  2:458143/1‑140 (MQ=255)

 atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATgccgcc                                                                >  1:313211/1‑140 (MQ=255)

 atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATgccgcc                                                                >  2:354784/1‑140 (MQ=255)

 atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATgccgcc                                                                >  2:345460/1‑140 (MQ=255)

 atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATgccgcc                                                                >  2:259421/1‑140 (MQ=255)

  tcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCca                                                               >  2:131630/1‑140 (MQ=255)

        gACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGCCGGATGCCGCCACACCaa                                                         <  2:235203/140‑1 (MQ=255)

         aCTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAAc                                                        >  1:575109/1‑140 (MQ=255)

               aaCTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCC‑CGTAATATGGTCACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTgccg                                                 <  2:115890/140‑1 (MQ=255)

                       cAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCAc                                          >  2:93665/1‑140 (MQ=255)

                       cAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCAc                                          <  2:346832/140‑1 (MQ=255)

                       cAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCAc                                          >  2:322827/1‑140 (MQ=255)

                            cTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTCGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCTCCACCGAtt                                     >  2:177509/1‑140 (MQ=255)

                               ttGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTa                                  >  2:567581/1‑140 (MQ=255)

                               ttGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTa                                  >  2:358429/1‑140 (MQ=255)

                                 gCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAAt                                <  1:457354/140‑1 (MQ=255)

                                  cGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATc                               >  1:92726/1‑140 (MQ=255)

                                  cGTTGACCGAATCTACTGGGAGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATc                               >  1:385042/1‑140 (MQ=255)

                                     tGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATcaca                            <  1:137455/140‑1 (MQ=255)

                                       aCCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACAtt                          <  1:345460/140‑1 (MQ=255)

                                       aCCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACAtt                          >  1:531712/1‑140 (MQ=255)

                                          gAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGa                       <  1:46934/140‑1 (MQ=255)

                                            aTCTACTGGGTGGGGGGGTGATTGATCCTCCCCACGTAATATGGACAAAGCCGTACGCGGGGTTCTTGTTTTCAAATTGTTCCGGACTGACGCCGCCCCACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGata                     <  2:292999/140‑1 (MQ=14)

                                            aTCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGata                     <  1:322827/140‑1 (MQ=255)

                                            aTCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGata                     <  2:69012/140‑1 (MQ=255)

                                                 cTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAAtt                >  2:528465/1‑140 (MQ=255)

                                                     gtgggGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAac            >  1:199973/1‑140 (MQ=38)

                                                         ggggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACAcct        >  2:144199/1‑139 (MQ=21)

                                                             cTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGc    <  1:458143/140‑1 (MQ=17)

                                                               gattgatCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGccc  <  1:390186/140‑1 (MQ=14)

GATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCC  >  NC_000913/391643‑391845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A