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
A9 F174 I0 R1	34	41.4	875437	98.7%	864056	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,679,725	G→A	100%	W70* (TGG→TAG)	ssaA2_4 →	Staphylococcal secretory antigen ssaA2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,679,725	0	G	A	99.4%	123.7 / ‑6.8	41	W70* (TGG→TAG)	ssaA2_4	Staphylococcal secretory antigen ssaA2
Reads supporting (aligned to +/- strand): ref base G (0/1); major base A (17/21); minor base C (1/1); total (18/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
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.

AATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAA  >  USA300TCH1516_ALE/2679590‑2679858

aaTCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCCATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTAtt                                                                                                                                  <  1:500631/141‑1 (MQ=255)

    cGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACaa                                                                                                                              >  1:687874/1‑141 (MQ=255)

              aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTaaa                                                                                                                    <  1:631996/141‑1 (MQ=255)

              aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTaaa                                                                                                                    <  1:631940/141‑1 (MQ=255)

                  aTCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCaa                                                                                                                <  1:548336/141‑1 (MQ=255)

                  aTCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCaa                                                                                                                <  1:24168/141‑1 (MQ=255)

                       tCGCATGGCGCAGTTAATGATTAAAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATTGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAatat                                                                                                           <  1:229288/141‑1 (MQ=255)

                         gCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTGTTACAATGAACGTAAATCAAAATATGc                                                                                                         >  1:255481/1‑141 (MQ=255)

                                 cAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTTAATCAAAATATGCGACTGGTc                                                                                                 <  1:452538/141‑1 (MQ=255)

                                 cAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTc                                                                                                 <  1:94258/141‑1 (MQ=255)

                                        ttattaTAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTCGTATTACAATGGACGTAAATCAAAATATGCGACTGGTCGTACAcc                                                                                          >  1:588712/1‑141 (MQ=255)

                                            tataGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGa                                                                                      >  1:391260/1‑141 (MQ=255)

                                                         aaTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCa                                                                         >  1:805336/1‑141 (MQ=255)

                                                          aTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCAt                                                                        >  1:302262/1‑141 (MQ=255)

                                                          aTGTACATGGTGGGCATTTAAACGTCGCGAAAAAGTCAGTAAACCTATTTCTAATAGATGGGGCAATGCTAAAAATTAGTCTTTTTGTGTATAAATTTTAAAATATTCGACTGGTCGTACACCAAGAAAATTTGATGTcca                                                                        >  1:241579/1‑139 (MQ=255)

                                                             tACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTACACCTGTTCCTAGTAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCa                                                                     <  1:282560/141‑1 (MQ=255)

                                                                 tggtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCa                                                                 >  1:606374/1‑141 (MQ=255)

                                                                  ggttgGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCaa                                                                <  1:192395/141‑1 (MQ=255)

                                                                       gCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCa                                                           <  1:212656/141‑1 (MQ=255)

                                                                       gCATCTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACCCCAAGAAAATTTGCTGTCATGCAATCAACTGCa                                                           >  1:591764/1‑141 (MQ=255)

                                                                        cATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAg                                                          <  1:513173/141‑1 (MQ=255)

                                                                              aaCGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCGGGagagt                                                    >  1:155262/1‑137 (MQ=255)

                                                                                        acaAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGt                                          <  1:536254/141‑1 (MQ=255)

                                                                                        acaAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGt                                          <  1:754332/141‑1 (MQ=255)

                                                                                        acaAGTCGGTAAACCTGTTTCTAATAGAGGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCACGATATTATGGACATGt                                          <  1:433468/141‑1 (MQ=255)

                                                                                           aGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGc                                       <  1:223359/141‑1 (MQ=255)

                                                                                              cGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAgt                                    >  1:37689/1‑141 (MQ=255)

                                                                                               gggaacccTGTTTCTAATAGATGGGGCAATGCTAAAACATACAACTGTAAACCACGTAAATCAAAATATGCGACTGGGCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAgtt                                   <  1:282134/135‑1 (MQ=255)

                                                                                                gTATACCTGTTTCTAATAGAGGGGGTAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAATTATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGGAATCAACTGCAGGATATTATGGACATGTCGCAgttg                                  <  1:685750/141‑1 (MQ=255)

                                                                                                gTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAgttg                                  <  1:45344/141‑1 (MQ=255)

                                                                                                     ccTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGaa                             >  1:698627/1‑141 (MQ=255)

                                                                                                             tAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGtata                     <  1:715668/141‑1 (MQ=255)

                                                                                                                      gggCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACgg            >  1:298316/1‑141 (MQ=255)

                                                                                                                      gggCAATGCTAAAAACTAGTATTACGATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACgg            >  1:435618/1‑141 (MQ=255)

                                                                                                                       gggaaagCTAAAAATTAGGATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgt           <  1:98980/135‑1 (MQ=255)

                                                                                                                       ggCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCGTGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgt           >  1:284473/1‑141 (MQ=255)

                                                                                                                       ggCAAAGCTAACAATTCGCATTATAATGCACGTAAACCAAAATCTGCGTCTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAGAAACGgt           <  1:180026/141‑1 (MQ=255)

                                                                                                                         cAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgtag         >  1:449463/1‑141 (MQ=255)

                                                                                                                          aaTGCTAAACATTAGTATTACAATGCACGTAAATCAACATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgtagt        <  1:20809/141‑1 (MQ=255)

                                                                                                                                aaaaaTTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTaaa  >  1:99006/1‑141 (MQ=255)

                                                                                                                                aaaaaTTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTaaa  >  1:99086/1‑141 (MQ=255)

AATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAA  >  USA300TCH1516_ALE/2679590‑2679858

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