BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549133.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 13,629,696 number of mapped reads = 11,973,963 (87.85%) number of secondary alignments = 0 number of mapped bases = 475,462,181 bp number of sequenced bases = 475,417,698 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 599,700 duplication rate = 3.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5227 >>>>>>> ACTG content number of A's = 137,782,948 bp (28.98%) number of C's = 99,306,768 bp (20.89%) number of T's = 139,240,870 bp (29.29%) number of G's = 98,976,490 bp (20.82%) number of N's = 110,622 bp (0.02%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,529,765 number of insertions = 11,685 mapped reads with insertion percentage = 0.1% number of deletions = 35,467 mapped reads with deletion percentage = 0.3% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 0.1536X std coverageData = 0.8749X There is a 11.05% of reference with a coverageData >= 1X There is a 2.91% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 39021333 0.1565546069391739 1.8005242609033036 chr2 243199373 41004901 0.1686061131415828 0.800664477110229 chr3 198022430 32771938 0.16549609051863468 0.5311289200910029 chr4 191154276 31235007 0.16340208366565653 0.5479597995551722 chr5 180915260 29931727 0.16544611549075516 0.5451189781547279 chr6 171115067 27554696 0.16103021483198787 0.6001364004825892 chr7 159138663 26543219 0.16679302502371784 1.2445462058133898 chr8 146364022 24769404 0.1692315069067998 0.77111607877334 chr9 141213431 20071576 0.14213645159574093 0.7446109420211897 chr10 135534747 22870846 0.16874525910318777 0.7768076538369094 chr11 135006516 22210158 0.16451174845516345 0.7202614342399972 chr12 133851895 21826505 0.16306459464021783 0.5556263575571182 chr13 115169878 15240796 0.13233317829858254 0.46508171331047354 chr14 107349540 15114972 0.14080146035092464 0.6374129309637285 chr15 102531392 14000794 0.13655129153030518 0.4761085744269732 chr16 90354753 13851522 0.15330153135386249 0.5739660796941108 chr17 81195210 13038520 0.16058237918222024 0.5805410129143064 chr18 78077248 13109555 0.16790493179267793 1.5669124956793758 chr19 59128983 9598936 0.16233893283772527 1.4504681563266022 chr20 63025520 10266756 0.16289839417429638 0.5626082451767463 chr21 48129895 6347632 0.13188543212072248 0.5560349453292618 chr22 51304566 5706911 0.11123592781196122 0.47603925947128684 chrMT 16571 96983 5.852573773459659 7.254672418006247 chrX 155270560 15567584 0.10026101535281383 0.5394804989784416 chrY 59373566 3709910 0.062484203829023845 0.4631221966142955