BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068928.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,435,137 number of mapped reads = 2,090,613 (85.85%) number of supplementary alignments = 11,090 (0.46%) number of secondary alignments = 0 number of mapped bases = 136,514,037 bp number of sequenced bases = 136,452,040 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,590 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.041 >>>>>>> ACTG content number of A's = 36,861,739 bp (27.01%) number of C's = 23,522,458 bp (17.24%) number of T's = 45,179,678 bp (33.11%) number of G's = 30,556,523 bp (22.39%) number of N's = 331,642 bp (0.24%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,313,590 number of insertions = 12,544 mapped reads with insertion percentage = 0.59% number of deletions = 37,361 mapped reads with deletion percentage = 1.77% homopolymer indels = 48.06% >>>>>>> Coverage mean coverageData = 0.0441X std coverageData = 0.4285X There is a 3.83% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 15975766 0.06409519035862302 0.8152239514635923 chr2 243199373 9310076 0.038281661194907765 0.3648841804710769 chr3 198022430 8369584 0.042265838268927415 0.296694245342547 chr4 191154276 6203298 0.032451787790506975 0.22795316227246148 chr5 180915260 7219012 0.03990272572916182 0.22126014544080022 chr6 171115067 9963854 0.05822896939870292 0.3527284206188514 chr7 159138663 7288549 0.0457999889065299 0.34119388045328414 chr8 146364022 8418389 0.05751679193401777 0.5539153306739678 chr9 141213431 8048654 0.05699637734883731 0.4073232200587099 chr10 135534747 10027726 0.07398638520349324 0.8678596987283124 chr11 135006516 3995293 0.029593334591346686 0.3002485635405072 chr12 133851895 7046885 0.05264688258615988 0.2645284477439996 chr13 115169878 2909120 0.025259382492356205 0.17302464702358045 chr14 107349540 3895657 0.036289461510501116 0.2533204952203393 chr15 102531392 2418628 0.023589146239231785 0.1716227315214391 chr16 90354753 2456434 0.027186549887419868 0.2499745700670291 chr17 81195210 3045560 0.037509109219620224 0.2328299865567825 chr18 78077248 3048053 0.039038939999524576 0.682037994471847 chr19 59128983 2173701 0.03676202244168482 0.5117534040667527 chr20 63025520 1597467 0.025346351763539596 0.20000772370513895 chr21 48129895 2058079 0.042760928524776545 0.26514383315071877 chr22 51304566 886002 0.01726945706937663 0.15102155401850265 chrMT 16571 167051 10.080924506668277 6.634165691075571 chrX 155270560 9607455 0.06187557383704934 0.316934920209969 chrY 59373566 383744 0.006463212938902811 0.15315772489371327