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
A5 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,761,889	C→A	100%	D388Y (GAT→TAT)	fpgS ←	Folylpolyglutamate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,761,889	0	C	A	96.2%	98.8 / ‑3.0	37	D388Y (GAT→TAT)	fpgS	Folylpolyglutamate synthase
Reads supporting (aligned to +/- strand): ref base C (2/0); new base A (18/16); total (21/16)
Fisher's exact test for biased strand distribution p-value = 4.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01
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.

CTTCATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATCTACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGG  >  USA300TCH1516_ALE/1761754‑1762021

cttcATGGCTATTTTAGTTTTAGTTTTATAAGGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACGAAGGTATAACCTTGATAATTTTTTATACATTCAACGTAGCCATatact                                                                                                                                  >  2:55662/1‑140 (MQ=255)

  tcATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTaa                                                                                                                                >  1:274941/1‑140 (MQ=255)

  tcATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTaa                                                                                                                                >  1:485626/1‑140 (MQ=255)

   tattgCTATTTTATTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAAt                                                                                                                               <  1:503362/136‑1 (MQ=255)

    aTGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATAAAGACTACCGGTAATTACTAATGTATAAACTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAAtt                                                                                                                              >  1:344485/1‑140 (MQ=255)

     tGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTATGAATATACTAATTg                                                                                                                             >  2:194223/1‑140 (MQ=255)

            tttagttttagtTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATAACATTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTATATTtca                                                                                                                      >  1:59316/1‑140 (MQ=255)

               agttttagttttATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTtcatca                                                                                                                   >  2:92897/1‑140 (MQ=255)

               agttttagttttATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTtcatca                                                                                                                   >  2:450585/1‑140 (MQ=255)

                   ttagttttaTAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCAGATACTAATTGTATTTCATCAtttt                                                                                                               <  1:352826/140‑1 (MQ=255)

                               tGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATActaccta                                                                                                   <  2:228610/140‑1 (MQ=255)

                               tGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATActaccta                                                                                                   <  1:407120/140‑1 (MQ=255)

                               tGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATActaccta                                                                                                   <  1:280700/140‑1 (MQ=255)

                                 cTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACa                                                                                                 <  1:364391/140‑1 (MQ=255)

                                 cTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACa                                                                                                 <  2:511374/140‑1 (MQ=255)

                                    cAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTCGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAAtt                                                                                              <  2:275611/140‑1 (MQ=255)

                                         tCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCATTTTTATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATttcttc                                                                                         <  1:181853/140‑1 (MQ=255)

                                                 tGATTTAGCTTCACTTATGAGATACAGACTACCGGTAATTACTACTGTATCACCTTGATAATTTTTTATAAATTAAACGTAGTCATGTCCTAATGGTATTTCATCATTTTCAATACTACCTACAAGTTCTTCTTTTCGTa                                                                                 >  1:345126/1‑140 (MQ=255)

                                                    tttAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCTATACTACCTACAATTACTTCTTTGCGTAACg                                                                              >  1:96925/1‑140 (MQ=255)

                                                     ttAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTAAACTTTCTTCTTTGCTTCACGc                                                                             >  2:310660/1‑140 (MQ=255)

                                                            cACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGa                                                                      >  1:532295/1‑140 (MQ=255)

                                                               ttATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGaaaa                                                                   <  1:441974/140‑1 (MQ=255)

                                                                   gAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTAATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCaa                                                               >  1:44/1‑140 (MQ=255)

                                                                            acgaCCGTTAATTACTGATGTATCCCCTTGATAATTTTTTATTAAATCAACGTAGTCATATATTCATCGTATTTCATCATTTTCAATACTACCTATAATTTCTTCTTTGCGTAACGCTTTCGGAACATTAAATTCAGttt                                                      >  2:204563/4‑139 (MQ=255)

                                                                            aCTACCGGTAATTACTAATGTATCACCTTGATAATTTGTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATGTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTTGGAAAATCAAATTCAGTTg                                                      >  2:143434/1‑140 (MQ=255)

                                                                             cTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGc                                                     <  1:230994/140‑1 (MQ=255)

                                                                              tACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCa                                                    <  1:345931/140‑1 (MQ=255)

                                                                                    tAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCCACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAAc                                              <  1:457019/140‑1 (MQ=255)

                                                                                          ttAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGCAGTGCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATgc                                        <  1:126173/139‑1 (MQ=255)

                                                                                               gTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAAt                                   <  1:205422/140‑1 (MQ=255)

                                                                                                     ccTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGGAAATCATCATTTTCAATACTAACTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACt                             >  1:429032/1‑140 (MQ=255)

                                                                                                         gATAGTTTTTTATAAATTCAACGTAGTCATCTACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTaaa                         >  2:335365/1‑140 (MQ=255)

                                                                                                                   tataAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGAAATTAAACTTAAATGTTTGAcct               >  2:319475/1‑139 (MQ=255)

                                                                                                                    ataAATTCAACGTAGTCATCTACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTATTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAGATGTTTCACCAt              >  2:396281/1‑140 (MQ=255)

                                                                                                                      aaaTTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCAtct            >  2:449497/1‑140 (MQ=255)

                                                                                                                              cGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATc    >  1:176537/1‑140 (MQ=255)

                                                                                                                               gTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCg   <  2:128320/140‑1 (MQ=255)

                                                                                                                                tAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTTCGTAACGCTTTCGGAAAATCAAATACAGTTGCATAAAACATATGCGCAATTAAACTTAAATGTTTGACCATCACGTTAATCgg  >  1:233655/1‑140 (MQ=255)

CTTCATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATCTACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGG  >  USA300TCH1516_ALE/1761754‑1762021

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