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
A15 F59 I0 R1	41	74.1	1560052	97.4%	1519490	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,856,087	T→A	100%	P80P (CCT→CCA)	USA300HOU_2698 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,856,087	0	T	A	100.0%	172.6 / NA	54	P80P (CCT→CCA)	USA300HOU_2698	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (22/32); total (22/32)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATTC  >  CP000730/2855952‑2856223

gaTGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACg                                                                                                                                     <  2:456296/141‑1 (MQ=255)

gaTGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACg                                                                                                                                     >  2:635339/1‑141 (MQ=255)

  tGCATGGCGTTGGTCCTAAAGCTATATCAATATGGGAACAAGCTTTATTTCAGGACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTc                                                                                                                                   >  2:620931/1‑141 (MQ=255)

         cGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAAt                                                                                                                            <  1:212781/141‑1 (MQ=255)

          gTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATg                                                                                                                           <  1:631025/141‑1 (MQ=255)

             ggTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATa                                                                                                                        <  1:581454/141‑1 (MQ=255)

                       cTATATCAATAGTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAg                                                                                                              <  2:768397/141‑1 (MQ=255)

                           atCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgttgt                                                                                                          <  2:302760/141‑1 (MQ=255)

                                tatTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcag                                                                                                     <  1:455510/141‑1 (MQ=255)

                                 atTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcagc                                                                                                    <  1:635339/141‑1 (MQ=255)

                                  ttGGAACATGCTTTATTTCAGCACAAACTACATTTTAAAACGGGAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcagca                                                                                                   <  2:331997/141‑1 (MQ=255)

                                    ggAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACagcagc                                                                                                 <  1:92457/141‑1 (MQ=255)

                                    ggAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACagcagc                                                                                                 >  1:475432/1‑141 (MQ=255)

                                     gAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAgcagca                                                                                                <  1:387976/141‑1 (MQ=255)

                                      aaCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTCAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTCCAGCAGAAt                                                                                               >  2:188896/1‑141 (MQ=255)

                                       aCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCGTCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCAtt                                                                                              >  1:149757/1‑141 (MQ=255)

                                       aCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACACCAGCAtt                                                                                              >  1:380712/1‑141 (MQ=255)

                                        cAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTa                                                                                             <  2:220761/141‑1 (MQ=255)

                                           gCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTTTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACATCAGCATTAAat                                                                                          >  2:193003/1‑141 (MQ=255)

                                               tATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTg                                                                                      >  2:247478/1‑141 (MQ=255)

                                               tATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTAATAGTTGTTACAGTAGCATTAGATATTg                                                                                      <  2:516134/141‑1 (MQ=255)

                                                  ttCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAat                                                                                   <  2:626452/141‑1 (MQ=255)

                                                      gCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGGTGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAattatt                                                                               >  2:397389/1‑141 (MQ=255)

                                                      gCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAattatt                                                                               >  1:268007/1‑141 (MQ=255)

                                                         ccAACTAGATTTTAAAACTGAATTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGTCAATACGTCAACAAATGATAGATTTTAGAGTTGTTACAGCAGCATTAGATATTGAATTATTACg                                                                            <  1:653397/141‑1 (MQ=255)

                                                          cAACTACATTTTACAACGGAAGTTCCGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAACACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTCAATTATTACGt                                                                           >  2:250746/1‑141 (MQ=255)

                                                           aaCTACATTTTAAAACGGAAGTTCAGTGATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGtt                                                                          <  2:603802/141‑1 (MQ=255)

                                                            aCTACCTTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTc                                                                         <  2:681116/141‑1 (MQ=255)

                                                              tagaTTTTAAAACGGAAGTTGGGTCATCATTACCTTTTAAGTTAACAGGCAATTTTTCATCTACTCATGGGCCAAAAGGTCTGCAAATGATAGATGGTAGTGAGGTATCAGCAGCATTAGATATTGATCTAGTACGTTGAc                                                                       <  2:134516/138‑1 (MQ=255)

                                                               aCATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACt                                                                      >  1:750630/1‑141 (MQ=255)

                                                                aaTTTTAAAACGGAAGTTCAGGCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTg                                                                     <  1:70537/140‑1 (MQ=255)

                                                                         aCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTacaaca                                                            >  1:82683/1‑141 (MQ=255)

                                                                             gaGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGAAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAat                                                        >  2:558353/2‑141 (MQ=255)

                                                                               gTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGTGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAattt                                                      <  2:54753/141‑1 (MQ=255)

                                                                                 tCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAatttat                                                    >  1:551171/1‑141 (MQ=255)

                                                                                     tcatcaTTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAGTTTAGTTgg                                                >  2:500596/1‑141 (MQ=255)

                                                                                      catcatTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTTTTTGGt                                               >  2:416221/1‑141 (MQ=255)

                                                                                              ccTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAAGGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTCGGTCTGTCCCt                                       <  1:141021/141‑1 (MQ=255)

                                                                                                ttttAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTgg                                     <  2:64063/141‑1 (MQ=255)

                                                                                                 tttAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATCGAATTATTACGTTCACTGGTTACAACAGAATTTATGTGGTCTGTCCCTGGc                                    <  2:551171/141‑1 (MQ=255)

                                                                                                  ttcaGTTAACAGGAGACGTGGCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGcc                                   <  2:212634/138‑1 (MQ=255)

                                                                                                   tAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCg                                  >  1:97793/1‑141 (MQ=255)

                                                                                                               ggaTGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACAtata                      <  2:664004/140‑1 (MQ=255)

                                                                                                                 aagtgtCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACg                    <  2:577777/139‑1 (MQ=255)

                                                                                                                  tgtgTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACgtatcagg                   >  1:134933/1‑137 (MQ=255)

                                                                                                                    tgtCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTTACTGGTTATAACAGAATTTATTTGGTCTGTACCTGGCCGCTTTGACATATACGGAc                 >  1:30491/1‑141 (MQ=255)

                                                                                                                    tgtCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGAc                 >  1:740692/1‑141 (MQ=255)

                                                                                                                      tCATGCAATCCTGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCt               <  1:118010/141‑1 (MQ=255)

                                                                                                                             aTCATTCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTTCAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAatat        <  1:151426/141‑1 (MQ=255)

                                                                                                                             aTCATGCGCCAAAGCGTGAACGAATGATAGATTTTATCGTTGTTACAGCAGCATTAGTTTTTGAATTAGTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATGTACGGACCTCAAatat        <  2:249916/141‑1 (MQ=255)

                                                                                                                             aTCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAatat        <  2:402615/141‑1 (MQ=255)

                                                                                                                               cATGCGCCAAAAAGTCAACAAATGATAGATTTTATAGCTGTTACAGCAGCATAACATAGTAAATTATTACGTTCACTGGTTACAACAGAGTATATTTGGGCTGTACCTGGCCGTTATGACATATACGGACCTccacaactt      >  2:446577/1‑133 (MQ=255)

                                                                                                                                aTGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTaa     <  1:247478/141‑1 (MQ=255)

                                                                                                                                   cgcCAAAACGTCAACAAATGATAGATTTGATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATTc  <  1:538890/141‑1 (MQ=255)

GATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATTC  >  CP000730/2855952‑2856223

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A