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
A12 F1 I1 R1	760	58.2	3022526	90.8%	2744453	102.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	391,739	C→T	289 (TAG→TAA)	insF1 ←	IS3 transposase B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	391,739	0	C	T	100.0%	130.3 / NA	43	289 (TAG→TAA)	insF1	IS3 transposase B
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (25/18); total (25/18)

AGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCC  >  NC_000913/391624‑391845

aGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     <  1:227428/139‑1 (MQ=255)

  aTGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAAtt                                                                                   >  1:757533/1‑139 (MQ=255)

      cTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTc                                                                               >  1:863583/1‑139 (MQ=255)

         cGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCgg                                                                            >  1:770812/1‑139 (MQ=255)

          gTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGa                                                                           <  2:770812/139‑1 (MQ=255)

                   gATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgccg                                                                  >  1:431259/1‑139 (MQ=255)

                    atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCTAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgccgc                                                                 >  1:927570/1‑139 (MQ=255)

                    atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAg                                                                                                        >  1:328046/1‑100 (MQ=255)

                    atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAg                                                                                                        <  2:328046/100‑1 (MQ=255)

                          tGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACAcc                                                           <  2:863583/139‑1 (MQ=255)

                                 tAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACtgtg                                                    <  2:444848/139‑1 (MQ=255)

                                   aCTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCATCTGTgcc                                                  >  2:335200/1‑139 (MQ=255)

                                        tACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGa                                                                       <  2:1109959/113‑1 (MQ=255)

                                        tACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGa                                                                       >  1:1109959/1‑113 (MQ=255)

                                                 gTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCATCTGTGCCGCCGCCACCGATTg                                    <  1:335200/139‑1 (MQ=255)

                                                 gTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTg                                    >  2:242311/1‑139 (MQ=255)

                                                  ttGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     <  2:1235969/89‑1 (MQ=255)

                                                  ttGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     >  1:1235969/1‑89 (MQ=255)

                                                  ttGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAgg                                                                     <  2:551529/105‑1 (MQ=255)

                                                  ttGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAgg                                                                     >  1:551529/1‑105 (MQ=255)

                                                  ttGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGt                                   >  2:407287/1‑139 (MQ=255)

                                                  ttGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGt                                   >  2:1259595/1‑139 (MQ=255)

                                                   tGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGGTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTa                                  >  1:898813/1‑139 (MQ=255)

                                                       ttGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCt                                                                                               >  2:381381/1‑74 (MQ=255)

                                                       ttGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCt                                                                                               <  1:381381/74‑1 (MQ=255)

                                                       ttGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATca                              >  1:1376327/1‑139 (MQ=255)

                                                         gACCGAATCTACTGGGTGGGGGGCTGATTGAATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATcac                             >  2:657488/1‑139 (MQ=255)

                                                         gACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATcaca                            <  2:1376327/139‑1 (MQ=255)

                                                           ccGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACAtt                          <  2:757533/139‑1 (MQ=255)

                                                              aaTCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGAGTGAGGCCGCTACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGa                       <  2:927570/139‑1 (MQ=255)

                                                                         tgggGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGa                                       <  2:411008/112‑1 (MQ=255)

                                                                         tgggGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGa                                       >  1:411008/1‑112 (MQ=255)

                                                                           gggggCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTaa                                 >  1:756957/1‑116 (MQ=38)

                                                                           gggggCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTaa                                 <  2:756957/116‑1 (MQ=37)

                                                                           gggggCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAacgc          >  1:630257/1‑137 (MQ=25)

                                                                            ggggCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACGcc         >  2:945927/1‑139 (MQ=21)

                                                                              ggCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTgccgccg                                              <  1:747499/100‑1 (MQ=25)

                                                                              ggCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTgccgccg                                              >  2:747499/1‑100 (MQ=21)

                                                                               gCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACGCCGtt      <  1:945927/139‑1 (MQ=17)

                                                                                 tgattg‑atCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACGCCGTTGc    >  2:444791/1‑139 (MQ=17)

                                                                                   attg‑atCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     <  2:784749/56‑1 (MQ=9)

                                                                                   attg‑atCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     >  1:784749/1‑56 (MQ=255)

                                                                                   attg‑atCCTACCCACGTAATATCGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGACCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACGCCGTTGccc  >  2:817134/1‑139 (MQ=2)

AGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGCTGATTG‑ATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCC  >  NC_000913/391624‑391845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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