BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3087919.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,911,283 number of mapped reads = 1,126,904 (58.96%) number of supplementary alignments = 5,672 (0.3%) number of secondary alignments = 0 number of mapped bases = 69,617,586 bp number of sequenced bases = 69,596,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,655 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1238 >>>>>>> ACTG content number of A's = 20,209,550 bp (29.04%) number of C's = 13,372,682 bp (19.21%) number of T's = 20,671,843 bp (29.7%) number of G's = 15,341,422 bp (22.04%) number of N's = 769 bp (0%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 586,699 number of insertions = 4,840 mapped reads with insertion percentage = 0.43% number of deletions = 13,663 mapped reads with deletion percentage = 1.2% homopolymer indels = 45.68% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.1938X There is a 2.07% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 6000796 0.024075350247572704 0.28059852173424593 chr2 243199373 6447597 0.026511569172507694 0.2267244191090862 chr3 198022430 4872732 0.024606970028597266 0.16694071312131606 chr4 191154276 4666986 0.024414761195297563 0.1681487602882138 chr5 180915260 4119553 0.022770622002809493 0.16021259059658524 chr6 171115067 3790998 0.02215467092678636 0.17503123599122986 chr7 159138663 3603209 0.02264194591103232 0.20484969823348098 chr8 146364022 3300296 0.02254854680066116 0.20490830976323388 chr9 141213431 2880690 0.020399546839138836 0.17985752214511228 chr10 135534747 3550790 0.026198374059753105 0.21100494281746304 chr11 135006516 3069196 0.02273368790584893 0.18065947782364467 chr12 133851895 3014907 0.022524201095546686 0.16000328433051103 chr13 115169878 2013872 0.01748609996791001 0.1405010990921558 chr14 107349540 1956794 0.018228247647824106 0.14799966034802473 chr15 102531392 2225969 0.021710121715698544 0.15855268253048957 chr16 90354753 2150176 0.02379704363753836 0.17429382879837413 chr17 81195210 1695486 0.020881601266872763 0.16875659245211186 chr18 78077248 2011820 0.025767045477832415 0.3243874249174252 chr19 59128983 1183687 0.020018727533331667 0.21556103981591054 chr20 63025520 1269206 0.020137969508224603 0.1525929254748107 chr21 48129895 889582 0.018482940800099396 0.14794537463226987 chr22 51304566 737779 0.014380376982430764 0.12609879632113374 chrMT 16571 37301 2.2509806288093657 1.9522415546033718 chrX 155270560 3967324 0.025551038136270004 0.1817851262933027 chrY 59373566 160840 0.002708949635937313 0.06467923915809606