BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716196.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,970,741 number of mapped reads = 1,767,067 (89.67%) number of supplementary alignments = 43,763 (2.22%) number of secondary alignments = 0 number of mapped bases = 132,017,970 bp number of sequenced bases = 131,973,087 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,173 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8424 >>>>>>> ACTG content number of A's = 33,893,007 bp (25.68%) number of C's = 27,122,543 bp (20.55%) number of T's = 39,442,943 bp (29.89%) number of G's = 31,498,768 bp (23.87%) number of N's = 15,826 bp (0.01%) GC percentage = 44.42% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 972,753 number of insertions = 11,845 mapped reads with insertion percentage = 0.66% number of deletions = 25,632 mapped reads with deletion percentage = 1.43% homopolymer indels = 40.76% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.3386X There is a 3.66% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.08% 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% 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 10418827 0.04180060598525048 0.36818164002403686 chr2 243199373 11195075 0.04603249943411655 0.509971815197608 chr3 198022430 8851379 0.04469887072893712 0.23962813278714085 chr4 191154276 8401510 0.04395146253490034 0.25779164045054026 chr5 180915260 7906685 0.04370380364818313 0.23766272209350844 chr6 171115067 7584607 0.04432460059171762 0.27159816943566667 chr7 159138663 7224140 0.045395253823390484 0.41516446593464396 chr8 146364022 6766202 0.04622858751449178 0.4334244440994129 chr9 141213431 5591468 0.03959586535362915 0.36399173134044416 chr10 135534747 6225469 0.04593264190768733 0.32297957506290076 chr11 135006516 5992019 0.04438318369759279 0.3762948113145208 chr12 133851895 5996941 0.04480280985188891 0.24407224394842936 chr13 115169878 4155266 0.036079451260684674 0.21516063000469704 chr14 107349540 4019201 0.0374403187941001 0.2594687137133291 chr15 102531392 3843971 0.03749067407570161 0.22172249147552625 chr16 90354753 3953951 0.04376029891864128 0.2604582766679931 chr17 81195210 3692625 0.04547836011508561 0.2637049317201101 chr18 78077248 3590549 0.04598713571461945 0.6642387308310206 chr19 59128983 2777102 0.04696684872797491 0.35046204380952944 chr20 63025520 2868279 0.04550980301312865 0.2526875423455852 chr21 48129895 1738491 0.036120814308861465 0.23920820250933053 chr22 51304566 1549409 0.030200216487553954 0.1987247228429594 chrMT 16571 3775 0.2278076157141995 0.5746690486475124 chrX 155270560 7334758 0.04723856215885355 0.3061393127399448 chrY 59373566 336271 0.005663648364997986 0.15939150507904049