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
A13 F121 I0 R1	43	32.8	695000	96.9%	673455	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,232,465	G→C	100%	A124P (GCG→CCG)	USA300HOU_1157 →	non‑specific serine/threonine protein kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,232,465	0	G	C	100.0%	95.8 / NA	32	A124P (GCG→CCG)	USA300HOU_1157	non‑specific serine/threonine protein kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (19/13); total (19/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAGAAGATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATGCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATCAT  >  CP000730/1232328‑1232599

aagaagATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGTATGGCATTAAACATccga                                                                                                                                     >  1:237985/1‑140 (MQ=255)

  gaagaTGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAGTCAAATATTGGATGGCATTAAACATCCGCAt                                                                                                                                   >  1:119668/1‑141 (MQ=255)

      aTGACTGTTACTACTTAATAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATGAAGTGTTGACACAGCGATTAATTTTACGAATCAAATAGGGGATGGCATTAAACATCCGCATGata                                                                                                                               <  2:89014/141‑1 (MQ=255)

         aCTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGc                                                                                                                            <  2:125096/141‑1 (MQ=255)

         aCTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGc                                                                                                                            >  1:30774/1‑141 (MQ=255)

           tGTTACTACTTAGTAATGGAATATATTGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGt                                                                                                                          >  2:226669/1‑141 (MQ=255)

           tGTTACTACTTAGTAATGGAATATAACGAAGGTCCGACTTTGTCTGAGCATATTAAAAGTCACGGGCAATTAAGTGTTGACACAGCGATTAATTTAACGAATCAAATATTGGATGGCATTAAAAATCCGCATGAAATGCGt                                                                                                                          >  2:1561/1‑141 (MQ=255)

                ctattTAGTAATGAAATATATCGAAGGTCAGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAAGCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGt                                                                                                                     <  1:342198/141‑1 (MQ=255)

                    gtAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACAt                                                                                                                 >  2:201781/2‑141 (MQ=255)

                        tAATGGAATATATCGTAGGTCCGACTTTGTCTGAGTACATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATGTTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATagag                                                                                                             <  1:243118/141‑1 (MQ=255)

                            ggAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGatat                                                                                                         <  1:140691/141‑1 (MQ=255)

                             gAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATAtt                                                                                                        <  1:251967/141‑1 (MQ=255)

                               atatatCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTaa                                                                                                      >  2:127670/1‑141 (MQ=255)

                                  tatCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGCTGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGcc                                                                                                   >  2:220204/1‑141 (MQ=255)

                                             cGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGACTCAAATATTCGATGGCAGTAAACATCCGCGTGATCTGCGTATTGTCCAGCGAGATATTAGGCCCGAaaataaat                                                                                        >  2:309270/1‑141 (MQ=255)

                                             cGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAatatat                                                                                        <  1:226669/141‑1 (MQ=255)

                                               aCTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACCAAATATATTa                                                                                      >  2:220325/1‑141 (MQ=255)

                                                                tGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTAAATCAAAATTTTATTCCACAAAATATATTAATTGACAGCAATAAAAc                                                                     >  1:177982/1‑141 (MQ=255)

                                                                tGAAAGTCATGGGCAATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAAc                                                                     >  1:183616/1‑141 (MQ=255)

                                                                tGAAAGTCATGGGCAATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAAc                                                                     >  1:183615/1‑141 (MQ=255)

                                                                       cATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGaaa                                                              >  2:250583/1‑141 (MQ=255)

                                                                        aTGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGaaaa                                                             >  1:56963/1‑141 (MQ=255)

                                                                        aTGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGAACGCAATAAAACGTTGaaaa                                                             >  2:266653/1‑141 (MQ=255)

                                                                        aTGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGACACAAAATATATTAATTGACAGCAAAAAAAcctagtgaa                                                             >  2:69992/1‑133 (MQ=255)

                                                                                     tgtgcacacAGGTATTAATTTTACGAATCAAATATTTGATGGCATTAAACACCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACACCAATAAAACGTTGAAAATATTTGATTTTgg                                                <  2:45859/136‑1 (MQ=255)

                                                                                         gACACAGCGATTAATGTTACGAATCAAATAGTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAGAATATATTAATTGACAGCAATAAAACGTTGAAAATGTTTGATTTTGGAAtt                                            >  1:156144/1‑141 (MQ=255)

                                                                                          acacAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTg                                           <  2:251703/141‑1 (MQ=255)

                                                                                               gCGATTAATTTTACGAAGCAAATATTGGATGGCATTAAACATCCGTATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTaaa                                      <  1:1561/141‑1 (MQ=255)

                                                                                                                acAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTc                     <  1:201781/140‑1 (MQ=255)

                                                                                                                 cAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCt                    >  2:93503/1‑141 (MQ=255)

                                                                                                                    atatTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTa                 <  1:270474/141‑1 (MQ=255)

                                                                                                                    atatTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTa                 >  1:146918/1‑141 (MQ=255)

                                                                                                                                   aaaCATCCTTATGATATGCGTAGTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATCAt  <  2:138176/141‑1 (MQ=255)

AAGAAGATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATGCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATCAT  >  CP000730/1232328‑1232599

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