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
A3 F44 I0 R1	64	42.0	921266	98.7%	909289	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,124	G→A	34.2%	P174L (CCG→CTG)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,124	0	G	A	34.2%	42.0 / 28.6	35	P174L (CCG→CTG)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (8/15); new base A (7/5); total (15/20)
Fisher's exact test for biased strand distribution p-value = 2.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATC  >  USA300TCH1516_ALE/2027991‑2028245

atTAACTGTATAGTTAACCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAatat                                                                                                                    <  1:10221/141‑1 (MQ=255)

   aaCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAAc                                                                                                                 >  1:182593/1‑141 (MQ=255)

   aaCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTATTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAAc                                                                                                                 <  1:321990/141‑1 (MQ=255)

   aaCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTACATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAAc                                                                                                                 <  1:240666/141‑1 (MQ=255)

     cTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCt                                                                                                               <  2:446744/141‑1 (MQ=255)

     cTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCt                                                                                                               <  2:38661/141‑1 (MQ=255)

     cTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCt                                                                                                               <  1:184928/141‑1 (MQ=255)

     cTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCt                                                                                                               <  1:192681/141‑1 (MQ=255)

               aTCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTAcc                                                                                                     <  1:71714/141‑1 (MQ=255)

                   ggTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTaaa                                                                                                 >  1:401521/1‑141 (MQ=255)

                            atTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTa                                                                                        >  1:341586/1‑141 (MQ=255)

                              ttcttcAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTaac                                                                                      <  1:420889/141‑1 (MQ=255)

                                  tcAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAacaaca                                                                                  >  1:156593/1‑141 (MQ=255)

                                  tcAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAacaaca                                                                                  >  1:294385/1‑141 (MQ=255)

                                         gAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGtat                                                                           <  2:39809/141‑1 (MQ=255)

                                         gAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGtat                                                                           <  2:39840/141‑1 (MQ=255)

                                          aaTATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGtatt                                                                          >  1:26220/1‑141 (MQ=255)

                                          aaTATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGtatt                                                                          <  2:445052/141‑1 (MQ=255)

                                          aaTATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGtaat                                                                          >  1:453124/1‑139 (MQ=255)

                                          aaTATTGTTATTTTCAACATTATATGATTTTTCATTCACGTAAGTATTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGtatt                                                                          >  1:452505/1‑141 (MQ=255)

                                            tatTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGtattat                                                                        <  1:410962/141‑1 (MQ=255)

                                              ttGTTATTTTCAACTTTATATGATTTTTTATTTACGTATGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTAttt                                                                      >  2:45802/1‑141 (MQ=255)

                                                  tATTTTCAACTTTATATGATTTTTTTTTTTTTTTAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTTTCTAACAACAATGGTATTTTTTTctt                                                                  >  2:19890/1‑139 (MQ=255)

                                                                tatGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCt                                                    >  2:432542/1‑141 (MQ=255)

                                                                tatGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCt                                                    >  2:63298/1‑141 (MQ=255)

                                                                        ttcattcaCGTAAGTACTTCCATAAAAAGCAGCTACATGTAACTTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTaa                                            >  1:143955/1‑141 (MQ=255)

                                                                        ttcattcaCGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTaa                                            >  1:365805/1‑141 (MQ=255)

                                                                                    aGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAg                                >  2:62841/1‑141 (MQ=255)

                                                                                                      agcTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTg              <  1:354273/141‑1 (MQ=255)

                                                                                                                  aTTAATATTGTGATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATc  <  2:403281/141‑1 (MQ=255)

                                                                                                                  aTTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCGGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATc  <  2:211214/141‑1 (MQ=255)

                                                                                                                  aTTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATc  <  2:291471/141‑1 (MQ=255)

                                                                                                                  aTTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATc  <  1:286351/141‑1 (MQ=255)

                                                                                                                  aTTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATc  <  1:248189/141‑1 (MQ=255)

                                                                                                                  aTTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATc  <  2:82285/141‑1 (MQ=255)

ATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATC  >  USA300TCH1516_ALE/2027991‑2028245

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

GATK/CNVnator alignment

N/A