BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716401.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 = 2,176,438 number of mapped reads = 1,954,849 (89.82%) number of supplementary alignments = 9,999 (0.46%) number of secondary alignments = 0 number of mapped bases = 112,170,088 bp number of sequenced bases = 112,139,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,521 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.976 >>>>>>> ACTG content number of A's = 28,379,585 bp (25.31%) number of C's = 22,508,557 bp (20.07%) number of T's = 35,842,796 bp (31.96%) number of G's = 25,406,557 bp (22.66%) number of N's = 1,812 bp (0%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 601,459 number of insertions = 7,178 mapped reads with insertion percentage = 0.37% number of deletions = 18,535 mapped reads with deletion percentage = 0.94% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.3496X There is a 3.21% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 7968860 0.031971274406574095 0.6125934322407176 chr2 243199373 9449866 0.038856457084698155 0.4137431744754939 chr3 198022430 6783973 0.03425860898687083 0.20245468122554422 chr4 191154276 6887562 0.03603143044521798 0.22895678812659115 chr5 180915260 6197188 0.034254644964719944 0.20894911421737927 chr6 171115067 5840219 0.03413036094594756 0.23019300759425687 chr7 159138663 7155902 0.044966457962512855 0.48151135440632403 chr8 146364022 4904156 0.03350656761809948 0.3286646912615064 chr9 141213431 5171758 0.03662369764247141 0.38959210527467775 chr10 135534747 4278041 0.031564164132759254 0.32699491275265347 chr11 135006516 4314477 0.03195754640464909 0.2877471205109157 chr12 133851895 8294200 0.061965502991197845 0.31107177738595804 chr13 115169878 4155473 0.036081248605646696 0.20514280433135046 chr14 107349540 3977287 0.03704987464315171 0.24259751760920095 chr15 102531392 2825564 0.027558038029952818 0.1826897785480715 chr16 90354753 3156220 0.034931421925308126 0.230609749445315 chr17 81195210 3366114 0.04145705146892286 0.23297844187924047 chr18 78077248 3563438 0.04563990267689763 0.6891708434011472 chr19 59128983 1885050 0.031880304790630344 0.47562208831475616 chr20 63025520 3326391 0.05277847767063247 0.2610399857809563 chr21 48129895 1336917 0.027777268161503364 0.21925713747076772 chr22 51304566 1053399 0.02053226607549901 0.1546820305333798 chrMT 16571 26865 1.6212057208376078 1.7646819930272009 chrX 155270560 5941460 0.038265206230981584 0.27727113091024336 chrY 59373566 309708 0.00521626071777464 0.12070914326222924