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
A23 F59 I0 R1	88	34.1	751148	93.4%	701572	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%	97.6 / NA	36	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 (22/14); total (22/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAG  >  CP000730/1196372‑1196639

aTTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGc                                                                                                                                 <  1:336144/141‑1 (MQ=255)

     cGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGAAAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTACAGCAATGc                                                                                                                            >  2:220748/1‑141 (MQ=255)

      gtcaCAGTTATTAATCCTGAATTACAAGATGAGATTGCTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCa                                                                                                                           <  1:257439/138‑1 (MQ=255)

              ccataATCTTCAATTACCACTTGCGATTATTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAAGCTGGTAGCACTGGACTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTaa                                                                                                                   <  2:308856/138‑1 (MQ=255)

                     ccTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGaa                                                                                                            >  1:31606/1‑141 (MQ=255)

                            tACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCa                                                                                                     >  2:225715/1‑141 (MQ=255)

                            tACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACAGGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGAAAATACTTATAGCAATCCACCTTCTAAAGATGAATCATTCa                                                                                                     >  2:111418/1‑141 (MQ=255)

                             aCAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCAc                                                                                                    <  2:118263/141‑1 (MQ=255)

                              cAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACt                                                                                                   >  2:313686/1‑141 (MQ=255)

                               aaGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTAGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATAATTATAGCAATGCAACTTCTAAAGATGAATTATTCACtt                                                                                                  >  2:135822/1‑141 (MQ=255)

                                        ttgttgTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtcat                                                                                         >  1:321946/1‑141 (MQ=255)

                                              tAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATg                                                                                   >  1:104145/1‑141 (MQ=255)

                                              tAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATg                                                                                   >  1:96478/1‑141 (MQ=255)

                                                        tGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAAc                                                                         <  2:131537/141‑1 (MQ=255)

                                                         gCAACTGGTTTTAATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAACTACTTATAGCAATGAAACTTCTCTGGAAGGATCATTCGCTTCAAATTCATCAAATGCACAAGCAACt                                                                        >  1:193147/1‑141 (MQ=255)

                                                           aaCTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATTCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCCAATGCGCAAGCAACTGa                                                                      >  2:93795/1‑141 (MQ=255)

                                                           aaCTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGa                                                                      >  1:240257/1‑141 (MQ=255)

                                                                gTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAgtg                                                                 <  1:330921/141‑1 (MQ=255)

                                                                    tgatgaCTAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAg                                                             <  2:314893/141‑1 (MQ=255)

                                                                    tgatgaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGCTGAATCATTCACTTGAAATTCATCAAATGCACAAGCAACTGATAGTGTAAg                                                             >  1:152468/1‑141 (MQ=255)

                                                                     tatgaCAAACCAAGATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGt                                                            <  1:37553/140‑1 (MQ=255)

                                                                      atgaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTg                                                           >  1:359541/1‑141 (MQ=255)

                                                                       tgaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGa                                                          <  2:18409/141‑1 (MQ=255)

                                                                            aaCCAACATACAATGGACGTAACTCAGGGTGACCTGGATTCGGAACTAGCGCAAATACTTAAAGCTATGCAACATTTAAAGATGAATCATTAACTCAAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGaa                                                     >  2:165996/1‑141 (MQ=255)

                                                                             aCCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAac                                                    >  1:20707/1‑141 (MQ=255)

                                                                              ccAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAaca                                                   >  2:304417/1‑141 (MQ=255)

                                                                                  cATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATa                                               >  1:353878/1‑141 (MQ=255)

                                                                                    tCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATCGTGTAAGTGAAAGAACACATACa                                             >  2:92437/1‑141 (MQ=255)

                                                                                          ggccctAAATCCTGTAGCACTGTATTCTGAACAACCGTAAATTCCTATAGCAATGCAACTTCTAAAGATGAATCAGTCACTTCAAATTCATCAAATGCACAAGAAACTTATGCTGTAAGTGAAAGAACACATACAACTaaa                                       <  2:62132/136‑1 (MQ=255)

                                                                                                 aaTCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAgatg                                >  1:133159/1‑141 (MQ=255)

                                                                                                         aGCACTGGATTCGGAACAAGCGTAAATAGTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCt                        >  1:240634/1‑141 (MQ=255)

                                                                                                              tgtaTTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCtt                   <  2:130000/138‑1 (MQ=255)

                                                                                                                gATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCa                 <  1:313686/141‑1 (MQ=255)

                                                                                                                         cAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATa        <  2:368507/141‑1 (MQ=255)

                                                                                                                          aaGCGTAAATACTTATAGAAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTTATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATag       <  2:278407/141‑1 (MQ=255)

                                                                                                                               tAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGagaag  >  2:370351/1‑141 (MQ=255)

ATTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAG  >  CP000730/1196372‑1196639

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