BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716244.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 = 1,926,192 number of mapped reads = 1,765,285 (91.65%) number of supplementary alignments = 26,190 (1.36%) number of secondary alignments = 0 number of mapped bases = 138,959,817 bp number of sequenced bases = 138,901,533 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,104 duplication rate = 2.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.83 >>>>>>> ACTG content number of A's = 33,016,639 bp (23.77%) number of C's = 27,803,950 bp (20.02%) number of T's = 43,884,954 bp (31.59%) number of G's = 34,187,306 bp (24.61%) number of N's = 8,684 bp (0.01%) GC percentage = 44.63% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,141,786 number of insertions = 13,810 mapped reads with insertion percentage = 0.77% number of deletions = 32,828 mapped reads with deletion percentage = 1.83% homopolymer indels = 43.26% >>>>>>> Coverage mean coverageData = 0.0449X std coverageData = 0.5054X There is a 3.79% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 10990192 0.04409293728499878 0.7612083343855728 chr2 243199373 11741884 0.048280897500504655 0.77231154224146 chr3 198022430 8998500 0.045441821918860405 0.24757258242837196 chr4 191154276 8847071 0.046282359909123875 0.29210625783450966 chr5 180915260 8188985 0.04526420269909791 0.2519186344365895 chr6 171115067 7820566 0.045703549880852984 0.3112471901694861 chr7 159138663 7845931 0.04930248157231282 0.638141973318627 chr8 146364022 7075546 0.048342112380595825 0.6944746769339761 chr9 141213431 5935975 0.04203548457086918 0.5539082577076816 chr10 135534747 6726227 0.04962732545625367 0.5439630425333667 chr11 135006516 6172774 0.04572204500114646 0.49213299495438123 chr12 133851895 6287742 0.046975367812312256 0.2575898255949318 chr13 115169878 4209776 0.03655275210068382 0.216079772836697 chr14 107349540 4202228 0.039145281852162574 0.33273501713391684 chr15 102531392 3939044 0.03841793155407468 0.23044535940583807 chr16 90354753 4274312 0.047305889929221544 0.3014472141206396 chr17 81195210 4070431 0.050131417850880614 0.2967214284837598 chr18 78077248 3685144 0.0471986922489891 1.0929913295820657 chr19 59128983 3285261 0.05556092517268562 0.5647040632611808 chr20 63025520 2831757 0.04493032346262276 0.2729694208101773 chr21 48129895 1794224 0.03727878483840449 0.2547268269960134 chr22 51304566 1656508 0.03228773049166813 0.20642971054609327 chrMT 16571 5629 0.33968981956429906 0.6728834015145773 chrX 155270560 7956010 0.051239655476221634 0.3723521420805783 chrY 59373566 418100 0.0070418542824259535 0.2054197882249129