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
A17 F57 I0 R1	30	26.7	570066	96.5%	550113	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	95.0%	50.7 / ‑3.0	20	A124P (GCG→CCG)	USA300HOU_1157	non‑specific serine/threonine protein kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); major base C (9/10); minor base A (0/1); total (9/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.69e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAGAAGATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATGCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTA  >  CP000730/1232328‑1232584

aagaagATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAGGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTCCAGCTCAGATATTGGGTGGCCTTAAACATccgc                                                                                                                      >  2:198992/1‑141 (MQ=255)

 agaagaTGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTGACGAATCAAATATTGGATGGCGTTAAACATCCGCa                                                                                                                     >  1:7106/1‑141 (MQ=255)

      aTGACTGTTACTACTTAGTAATGGAATATATCGAGGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGata                                                                                                                <  2:208017/141‑1 (MQ=255)

        gACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGatagg                                                                                                              >  2:79868/1‑139 (MQ=255)

                    ttAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACaa                                                                                                  >  1:229626/1‑140 (MQ=255)

                                             cGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAatatat                                                                         >  2:139281/1‑141 (MQ=255)

                                                          gTATATTGAAAGTCAAGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCaa                                                            >  1:210933/1‑141 (MQ=255)

                                                                  aaaGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCGTTAAACATCCGCATGATATGCGTATTGTACATAGAGATAGTAAGCCACAAAATCTATTAAGTGACAGCAAAAAAACGt                                                    >  2:8692/1‑141 (MQ=255)

                                                                          gggCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATGAATTGACTGCAATAAAACGTTGAAAata                                            <  1:184148/141‑1 (MQ=255)

                                                                             ccATTAAGTGTTGACACAGCGATTTATTTTACGAATCAAATATTGGATGGCATTAGACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTCATTAACAGCAATAAAACGTTGAAAATAatt                                         >  2:27156/1‑141 (MQ=255)

                                                                              cATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTg                                        <  2:123467/141‑1 (MQ=255)

                                                                              cATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTg                                        <  1:211738/141‑1 (MQ=255)

                                                                                ttAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGAt                                      <  1:202887/141‑1 (MQ=255)

                                                                                ttAAGTGTTGAAACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGAt                                      <  1:239901/141‑1 (MQ=255)

                                                                                    gtgtTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTAACAGCAATAAAACGTTGAAAATATTTGATTTTg                                  >  2:85154/1‑141 (MQ=255)

                                                                                            acaGCGATTAATTTTACGAATAAAATATTGGATGGCATTAAACATACGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCt                          <  1:270310/141‑1 (MQ=255)

                                                                                                     aaTTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATCAAATCTTGGAATTGCTAAAGCttga                 >  2:212063/1‑139 (MQ=255)

                                                                                                            cGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTgaga          <  1:118484/141‑1 (MQ=255)

                                                                                                                acAAATATTGGAAGATATAAAACATCCAAAAGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTc      <  1:227866/140‑1 (MQ=255)

                                                                                                                  aaaTATTGAATGGCAGTAAATATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCtt    <  2:33998/141‑1 (MQ=255)

                                                                                                                    atatTGGATGACATTAAACATCCGAATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTa  <  1:274839/141‑1 (MQ=255)

AAGAAGATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATGCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTA  >  CP000730/1232328‑1232584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A