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 F73 I1 R1	29	53.4	1802238	99.2%	1787820	139.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,867,169	A→G	I128T (ATC→ACC)	rpoS ←	RNA polymerase, sigma S (sigma 38) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,867,169	0	A	G	100.0%	124.4 / NA	35	I128T (ATC→ACC)	rpoS	RNA polymerase, sigma S (sigma 38) factor
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/19); total (16/19)

CTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGC  >  NC_000913/2867033‑2867300

cTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCa                                                                                                                                  >  2:509245/1‑140 (MQ=255)

  ttACGATGTGAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGc                                                                                                                                >  1:366651/1‑140 (MQ=255)

        tgtgAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAgg                                                                                                                          <  1:639027/140‑1 (MQ=255)

          tgAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGtt                                                                                                                        >  1:551989/1‑140 (MQ=255)

           gAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTg                                                                                                                       <  1:334957/140‑1 (MQ=255)

                 gCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCctct                                                                                                                 >  2:710935/1‑140 (MQ=255)

                      cGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCG‑ATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATa                                                                                                           <  1:718156/140‑1 (MQ=255)

                      cGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGACGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGAt                                                                                                            >  1:147507/1‑140 (MQ=255)

                       gAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATa                                                                                                           <  1:836322/140‑1 (MQ=255)

                               cGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAg                                                                                                   >  2:391411/1‑140 (MQ=255)

                                                  cccGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTg                                                                                >  2:22295/1‑140 (MQ=255)

                                                               cTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGGGAGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCggg                                                                   <  2:868144/140‑1 (MQ=255)

                                                                       tCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAAttttt                                                           >  2:73642/1‑140 (MQ=255)

                                                                         caccaGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGGAAATTTTat                                                         >  2:550068/1‑139 (MQ=255)

                                                                               gTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAg                                                   <  1:394911/140‑1 (MQ=255)

                                                                                ttGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGa                                                  >  1:605877/1‑140 (MQ=255)

                                                                                ttGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGa                                                  <  1:329548/140‑1 (MQ=255)

                                                                                ttGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGa                                                  <  1:304918/140‑1 (MQ=255)

                                                                                 tGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGAc                                                 <  2:846264/140‑1 (MQ=255)

                                                                                 tGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGAc                                                 <  1:255192/140‑1 (MQ=255)

                                                                                  gCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACg                                                <  2:147507/140‑1 (MQ=255)

                                                                                    gTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCCGACGcc                                              >  2:378028/1‑139 (MQ=255)

                                                                                      aTGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAg                                            <  2:520659/140‑1 (MQ=255)

                                                                                          tGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTAc                                        <  2:325255/140‑1 (MQ=255)

                                                                                           gagaAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTAct                                       >  1:204507/1‑140 (MQ=255)

                                                                                           gagaAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTAct                                       <  1:391411/140‑1 (MQ=255)

                                                                                             gaAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTActct                                     >  2:134977/1‑140 (MQ=255)

                                                                                              aaGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACtctc                                    <  2:412593/140‑1 (MQ=255)

                                                                                                   gAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGatca                               >  1:649559/1‑140 (MQ=255)

                                                                                                                     aatcTTCTCTACCGCGGGGGTCAGCCCCAGGTTGCCCTTTTCGATAAGGTCAAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGa             <  2:686558/137‑1 (MQ=255)

                                                                                                                     aaaCTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGa             <  2:551989/140‑1 (MQ=255)

                                                                                                                     aaaCTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGa             <  2:346247/140‑1 (MQ=255)

                                                                                                                        cTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACAt          <  2:493165/140‑1 (MQ=255)

                                                                                                                        cTTCTCTACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACAt          <  1:550068/140‑1 (MQ=255)

                                                                                                                           ctctACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGGAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACAtctc       >  2:65235/1‑140 (MQ=255)

                                                                                                                              tACCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTGCCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACAGCTccgc    <  2:345903/140‑3 (MQ=255)

                                                                                                                               aCCGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACg   <  1:601003/140‑1 (MQ=255)

                                                                                                                                ccGCGCGGGTCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTTCCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGc  >  1:397922/1‑140 (MQ=255)

CTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAAGGTCCAGCAACGCCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGC  >  NC_000913/2867033‑2867300

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A