BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231764.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,833,588 number of mapped reads = 5,477,203 (93.89%) number of supplementary alignments = 41,152 (0.71%) number of secondary alignments = 0 number of mapped bases = 375,811,472 bp number of sequenced bases = 375,675,173 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 520,147 duplication rate = 4.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1908 >>>>>>> ACTG content number of A's = 101,113,054 bp (26.92%) number of C's = 69,297,270 bp (18.45%) number of T's = 109,590,449 bp (29.17%) number of G's = 95,591,561 bp (25.45%) number of N's = 82,839 bp (0.02%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 2,414,184 number of insertions = 25,776 mapped reads with insertion percentage = 0.47% number of deletions = 83,639 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.55% >>>>>>> Coverage mean coverageData = 0.1214X std coverageData = 31.9598X There is a 8.26% of reference with a coverageData >= 1X There is a 2.19% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.2% 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% 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 34315663 0.13767533602253293 1.7941734354864123 chr2 243199373 41149755 0.16920173145347706 113.97870593375902 chr3 198022430 25152632 0.1270191058659365 0.4676049803122821 chr4 191154276 19423118 0.10160964434821222 0.4528100290434575 chr5 180915260 22923723 0.126709725868343 0.4768576808274185 chr6 171115067 26612077 0.15552152984868364 0.7497079359912067 chr7 159138663 23972937 0.15064181480524313 1.9253323210262066 chr8 146364022 17940749 0.12257622300103231 1.148231160588939 chr9 141213431 13735563 0.09726810617610446 0.7254502650792078 chr10 135534747 17159031 0.12660244977621865 0.7050612633373415 chr11 135006516 15225013 0.11277243092474144 0.9789990950522446 chr12 133851895 13191762 0.0985549139965482 0.4289576425465886 chr13 115169878 13350330 0.11591859114411843 0.4521538553626775 chr14 107349540 14482394 0.1349087662602001 0.6226241463718111 chr15 102531392 9602935 0.09365848656380282 0.4042766121128953 chr16 90354753 11097504 0.12282147459359442 0.526567847159728 chr17 81195210 10248094 0.1262154996581695 0.6435730516486848 chr18 78077248 9064340 0.11609451193771583 1.5425479002669564 chr19 59128983 9314309 0.15752526979873813 1.263793121492226 chr20 63025520 7078816 0.11231666156820284 0.4681838518536608 chr21 48129895 7183659 0.14925565493130621 0.5685419195362853 chr22 51304566 3211153 0.06259000417233819 0.32069918807975706 chrMT 16571 36989 2.232152555669543 2.365952655904495 chrX 155270560 9664493 0.06224291971382083 0.43384660270078423 chrY 59373566 674433 0.011359145920256835 0.2155619591410332