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
A19 F166 I0 R1	50	63.8	1389156	94.9%	1318309	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,196,508	C→A	100%	intergenic (+2563/‑1229)	ftsQ → / → USA300HOU_1125	cell division protein FtsQ/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,196,508	0	C	A	100.0%	148.0 / NA	48	intergenic (+2563/‑1229)	ftsQ/USA300HOU_1125	cell division protein FtsQ/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (15/33); total (15/33)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAA  >  CP000730/1196372‑1196641

aTTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGc                                                                                                                                   >  1:277603/1‑141 (MQ=255)

      ggTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCa                                                                                                                             <  1:239171/141‑1 (MQ=255)

        tACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAGCAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAAc                                                                                                                           <  1:491661/141‑1 (MQ=255)

        tACAGTAATTAATCATGAATTACAAGATGAGATTGTTTTAACAGTTATTGCAACTGGTATTGATGACAAACCAACATCACATTGTCGTAAATCTCGTAGCACTAGAGTCGGAACAAGCGTAAATACTTATAGCAATGCAAc                                                                                                                           >  2:472404/1‑141 (MQ=255)

         aCAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACt                                                                                                                          <  2:52168/141‑1 (MQ=255)

          cggTTATGAATCCTGAAGTACAAGACGCGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACtt                                                                                                                         <  2:336184/139‑1 (MQ=255)

          aaGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACtt                                                                                                                         <  2:47714/140‑1 (MQ=255)

                 taATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGa                                                                                                                  <  2:218331/141‑1 (MQ=255)

                    tCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTATCGACGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGa                                                                                                               <  1:226313/141‑1 (MQ=255)

                    tCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGAAACTGGTTTTGGTGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGAAATGCAACTTCTAAAGATGa                                                                                                               >  1:196495/1‑141 (MQ=255)

                      cTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAAt                                                                                                             >  1:216216/1‑141 (MQ=255)

                      cTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATAATTATAGCAATGCAAATTCTAAAGATGAAt                                                                                                             >  1:272844/1‑141 (MQ=255)

                       tGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATc                                                                                                            <  2:113756/141‑1 (MQ=255)

                           ttACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTAGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTc                                                                                                        <  1:390872/141‑1 (MQ=255)

                              aaaGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACt                                                                                                     <  2:605164/140‑1 (MQ=255)

                               aaGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAAAACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACtt                                                                                                    >  1:10166/1‑141 (MQ=255)

                               aaGATGAGATTGTTGTAACAGTTATTGCAACTGGTTGTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACtt                                                                                                    <  1:584208/141‑1 (MQ=255)

                                      gaTTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtc                                                                                             >  1:79492/1‑141 (MQ=255)

                                           ttgtAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCAGTTCAAATTCATCaa                                                                                        <  1:364633/141‑1 (MQ=255)

                                                  ggTTATGTCAACTGGTTTTGAGGACAAACCAACAGCACATGGTCGTAAATCTGGTGGCGCTGGATTCGGAACAAGCGTAAATACTTAGAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGcaca                                                                                 <  2:24424/140‑1 (MQ=255)

                                                   gTTATTGCAACTGGTTCTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTCAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACaa                                                                                <  2:318932/141‑1 (MQ=255)

                                                       ttGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCaa                                                                            <  1:382666/141‑1 (MQ=255)

                                                       ttGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCaa                                                                            >  2:277647/1‑141 (MQ=255)

                                                       ttGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCaa                                                                            >  1:318596/1‑141 (MQ=255)

                                                            aCTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGAt                                                                       <  1:353262/141‑1 (MQ=255)

                                                             ttgtttttGATGACAAACCAACAGCACATGGTCGTAAATCTGGTAGCTCTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATa                                                                      <  2:514265/137‑1 (MQ=255)

                                                             cTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATa                                                                      <  2:216216/141‑1 (MQ=255)

                                                                      atgaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTg                                                             <  1:566024/141‑1 (MQ=255)

                                                                      atgaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTg                                                             <  1:640397/141‑1 (MQ=255)

                                                                      atgaCAAACCAACATCACAGGGTCGGAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTg                                                             <  2:98053/141‑1 (MQ=255)

                                                                         aCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGaaa                                                          >  2:281126/1‑141 (MQ=255)

                                                                          cAAACCAACATCACATGGTCGTATATCTGGTAGCACTGGATTCGGAACAAGCGTAAATTCTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCTACTGATAGTGTATGTGAAAg                                                         <  1:439157/141‑1 (MQ=255)

                                                                           aaaCCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGa                                                        >  2:399890/1‑141 (MQ=255)

                                                                             accaaactgacaTGGTCGGAAATCTGGTAGCACGGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGaaggggc                                                      <  2:255329/132‑6 (MQ=255)

                                                                             aCCAACATCACATGGTCGGAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAac                                                      <  2:281346/141‑1 (MQ=255)

                                                                                aaCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAAcaca                                                   <  1:690666/141‑1 (MQ=255)

                                                                                 aCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAAcacaa                                                  >  2:51428/1‑140 (MQ=255)

                                                                                        aTGGGCGTAAATCAGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTa                                           <  1:324256/141‑1 (MQ=255)

                                                                                           gTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAaag                                        <  1:65701/141‑1 (MQ=255)

                                                                                                  aTCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAgatga                                 <  1:498051/141‑1 (MQ=255)

                                                                                                   tCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAgatgat                                <  1:231334/141‑1 (MQ=255)

                                                                                                        gaGCACTGGATTCGGAACAAGCGTAAATACTGAGAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGGGAAAGAACACATACAACTAAAGAAGATGATATTcc                           <  1:312406/140‑1 (MQ=255)

                                                                                                             cTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCt                      >  2:220522/1‑141 (MQ=255)

                                                                                                              tGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCtt                     <  2:597004/141‑1 (MQ=255)

                                                                                                                gATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCa                   <  2:395435/141‑1 (MQ=255)

                                                                                                                gATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCa                   >  1:60690/1‑141 (MQ=255)

                                                                                                                                 aaaaCTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCCCAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAgaagaa  <  1:124184/138‑1 (MQ=255)

                                                                                                                                 aaTACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAgaagaa  >  2:41774/1‑141 (MQ=255)

ATTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAA  >  CP000730/1196372‑1196641

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A