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	2,709,600	(T)_5→4	100%	coding (1327/1812 nt)	USA300HOU_2562 ←	possible acetyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,709,596	0	T	.	100.0%	149.6 / NA	33	coding (1331/1812 nt)	USA300HOU_2562	possible acetyltransferase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (20/13); total (20/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCA  >  CP000730/2709458‑2709727

tatTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACttt                                                                                                                                   <  2:195041/141‑1 (MQ=255)

  ttGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATAACtttta                                                                                                                                 >  1:228835/1‑140 (MQ=255)

   tGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGTTGACttttca                                                                                                                                >  2:29693/1‑139 (MQ=255)

   tGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGGCACCAATTAATAGTGTTGATGACttttaa                                                                                                                                >  2:266174/1‑139 (MQ=255)

      gATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATTACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAatat                                                                                                                            >  1:7363/1‑141 (MQ=255)

         ttCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGGGGTGATGAC‑TTTTAATATCct                                                                                                                         >  1:242452/1‑141 (MQ=255)

          tCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCctc                                                                                                                        >  2:166599/1‑141 (MQ=255)

                     gtAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCg                                                                                                             >  1:29383/1‑141 (MQ=255)

                          aTCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTc                                                                                                        <  1:236353/141‑1 (MQ=255)

                           tCAACCAGTTGCCGTCCAACTTAACC‑CCAATATTGTGCATATGGTATTTTCTTAGTAAAGACATTAGCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCt                                                                                                       >  1:210821/1‑141 (MQ=255)

                                      ccGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTGTGCTATTCGCTGTCTGCTTATCctct                                                                                            <  2:171450/141‑1 (MQ=255)

                                       cGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCtt                                                                                           >  1:152378/1‑141 (MQ=255)

                                          ccAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCt                                                                                        <  1:131271/141‑1 (MQ=255)

                                             aCTTTACCATCATT‑TTGTTCATTTGGTATTTTCATAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTAt                                                                                     <  2:19414/141‑1 (MQ=255)

                                               tttACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCt                                                                                   >  1:272908/1‑141 (MQ=255)

                                                                gCATTTGGTATTTTCTTAGTAAAGACATTACCAATATTCACAATGACCGAGTGACCAAATAATAGTGGGGATTAC‑TTTTAATATCCTCTTTGCTATTCGCTGCCTGCTTTACGTCTTTCTTATCTTTTTTAACGCCttttt                                                                   >  1:60542/1‑141 (MQ=255)

                                                                  aTTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTttc                                                                 >  2:198141/1‑141 (MQ=255)

                                                                    ttGGGACTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTttctt                                                               <  1:26142/141‑1 (MQ=255)

                                                                            ttCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTTCTTATCTTTTTTAACGACTTTTttcttgctttttt                                                       >  2:63883/1‑133 (MQ=255)

                                                                              cTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTa                                                     <  2:43380/141‑1 (MQ=255)

                                                                               ttAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGGTGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATACTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTTTTTTaa                                                    >  2:83380/1‑141 (MQ=255)

                                                                                  gTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTTTTTTAAAtt                                                 >  2:125341/1‑141 (MQ=255)

                                                                                       gACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGtc                                            >  1:130154/1‑141 (MQ=255)

                                                                                        aCATTACCAATATCCACCATGACCGAGTCACAAAATAAAAGTGGTGATGAC‑TTTTAATATCCTATTTGCTATTAGCTGTCTGCGTATCCTCTTGCTTATCTTTTTTAACGTCTTTTTTCTTCGTTGTTTTAAATTCCGtct                                           >  2:210034/1‑141 (MQ=255)

                                                                                             aCCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGtcttcttc                                      <  1:287510/141‑1 (MQ=255)

                                                                                              ccAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TGTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGtctttttct                                     >  2:182267/1‑141 (MQ=255)

                                                                                                 atatCCACCATGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCtctt                                  <  1:287148/141‑1 (MQ=255)

                                                                                                      caccaTGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTttcttc                             <  1:263680/141‑1 (MQ=255)

                                                                                                       cccaTGACCGAGCCCCCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTtcttct                            <  1:178330/140‑1 (MQ=255)

                                                                                                       accaTGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTATTTTTCTCTTtcttct                            <  2:138662/141‑1 (MQ=255)

                                                                                                           tGACCGAGTCACCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGc                        <  1:256551/141‑1 (MQ=255)

                                                                                                                   tCACCAATTAATAGTTGTGATGAC‑TTTTAATATCCTCTTTTCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCAtgtt                <  1:166599/141‑1 (MQ=255)

                                                                                                                     aCCAATTAATAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCGtgttgt              >  2:171880/1‑141 (MQ=255)

                                                                                                                            aaTAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAGATTCCGTCTTCTTCTCTTTCTTCTTGGCTTCATGTTGTTTGCCag       >  1:155583/1‑140 (MQ=255)

                                                                                                                              tAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGt     >  1:271062/1‑141 (MQ=255)

                                                                                                                              tAGTGGTGATGAC‑TTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGt     >  1:64778/1‑141 (MQ=255)

                                                                                                                                 tggtgATGAC‑TTTTGATATACTCTTAGCTATTCGCTGTCTGCTTGTCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGttct  >  1:156647/1‑138 (MQ=255)

TATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAAT‑TTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCATGTTGTTTGCCAAGTGCA  >  CP000730/2709458‑2709727

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