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 F177 I0 R1	51	26.9	575130	96.6%	555575	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%	89.4 / ‑6.5	30	P80P (CCT→CCA)	USA300HOU_2698	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); major base A (10/19); minor base C (0/1); total (10/20)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAA  >  CP000730/2855957‑2856220

aTGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTcaac                                                                                                                             >  1:50716/1‑141 (MQ=255)

    cGTTGGTCCCAAAGCCATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAAt                                                                                                                         <  2:139223/141‑1 (MQ=255)

      ttGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACTTTTTAAAACGGAAGTTCAGTCATCATTACCTTTTACGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCGACAAATGa                                                                                                                       <  2:211385/141‑1 (MQ=255)

      ttGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGa                                                                                                                       <  1:264351/141‑1 (MQ=255)

      ttGGTCCGAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGa                                                                                                                       <  2:25293/141‑1 (MQ=255)

         gTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAg                                                                                                                    >  2:173158/1‑141 (MQ=255)

             tAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGGTAGAttt                                                                                                                <  1:230456/141‑1 (MQ=255)

                 tcTATATCAATATTGGAACAAGCTTTATTTCACCACCAACTACATTTTCAAACGGAAGATCAGTCATCATTAACTTTTAAGTTAAATGGAGATGTGTCATGCAATAATGAGCCAAAACGTCAACAAATGATAGATTTtatc                                                                                                            >  2:190751/2‑140 (MQ=255)

                 gCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAACTGATAGATTTtata                                                                                                            >  2:65219/1‑141 (MQ=255)

                 gCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTtata                                                                                                            >  2:193211/1‑141 (MQ=255)

                      atCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgttgt                                                                                                       <  2:217790/141‑1 (MQ=255)

                        cAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTGGTTa                                                                                                     >  1:279581/1‑141 (MQ=255)

                                   cAAGCTTTATTTCAGCAGCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCCTGAGAGAAGCCGACTTCATTTGCTAGATTTTATAGTTGTTAACGCAGCCttt                                                                                          >  1:78646/1‑140 (MQ=255)

                                           aTTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGa                                                                                  <  1:276720/141‑1 (MQ=255)

                                                       aCTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATCTTGAATTATTACGTTc                                                                      <  1:142187/141‑1 (MQ=255)

                                                              tttAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGtt                                                               <  1:10341/141‑1 (MQ=255)

                                                                        gaGTTCAGTCATCATTCCCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTGTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAat                                                     <  1:250856/140‑1 (MQ=255)

                                                                            tCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATCGCATTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAatttat                                                 >  1:281187/1‑141 (MQ=255)

                                                                                   tcatTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCt                                          <  1:193211/141‑1 (MQ=255)

                                                                                   tcatTACCTTTTAAGTTAACAGGAGACGTGTCAGGCAAGCATGCGACCCAACCTCAACAAATGATAGATTTTATAGTGGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCt                                          <  1:65219/141‑1 (MQ=255)

                                                                                      ttACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACCACAGAATTTAGTGGGTCTGTc                                       >  2:198915/1‑141 (MQ=255)

                                                                                            tttAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGc                                 <  1:204073/141‑1 (MQ=255)

                                                                                                      aaGGAGATGTGTCATGCAATCACGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACa                       <  2:265200/140‑1 (MQ=255)

                                                                                                              gtgtCATGCGATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTGGGTCTGTCCCTGGCCGCTTTGACATATACGGa               <  2:216001/141‑1 (MQ=255)

                                                                                                                gtCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGccc             >  2:256728/1‑141 (MQ=255)

                                                                                                                  cATGCAATTAGGCGCCAAAACGTCAACAAAGGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTc           <  1:107963/141‑1 (MQ=255)

                                                                                                                  cATGCAATCATGCGCCAAAACGTCAACTAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTc           <  1:18111/141‑1 (MQ=255)

                                                                                                                     gCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCaaa        <  2:281187/141‑1 (MQ=255)

                                                                                                                         tCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATAtt    <  1:259235/141‑1 (MQ=255)

                                                                                                                           aTGCGACAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTaa  <  2:27384/141‑1 (MQ=255)

ATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAA  >  CP000730/2855957‑2856220

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A