BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716413.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 = 849,261 number of mapped reads = 719,271 (84.69%) number of supplementary alignments = 3,107 (0.37%) number of secondary alignments = 0 number of mapped bases = 41,102,165 bp number of sequenced bases = 41,091,313 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,131 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7967 >>>>>>> ACTG content number of A's = 10,763,643 bp (26.19%) number of C's = 7,864,482 bp (19.14%) number of T's = 12,406,980 bp (30.19%) number of G's = 10,055,555 bp (24.47%) number of N's = 653 bp (0%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 202,464 number of insertions = 3,041 mapped reads with insertion percentage = 0.42% number of deletions = 6,960 mapped reads with deletion percentage = 0.96% homopolymer indels = 39.99% >>>>>>> Coverage mean coverageData = 0.0133X std coverageData = 0.1432X There is a 1.25% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4534066 0.0181907911876376 0.2011582386972002 chr2 243199373 3315650 0.01363346442509126 0.17996220306718447 chr3 198022430 3392148 0.017130120057611654 0.137170160097486 chr4 191154276 1775746 0.009289596011966795 0.10454087556552145 chr5 180915260 3123630 0.017265707713102808 0.13801058361848142 chr6 171115067 3259474 0.019048433648452476 0.17156598616506802 chr7 159138663 2226447 0.013990610188801197 0.169507563123802 chr8 146364022 2754273 0.01881796470446815 0.1498621266158874 chr9 141213431 1614657 0.011434160253496 0.13010092037094637 chr10 135534747 1956639 0.014436438207244376 0.15252987922799244 chr11 135006516 1298816 0.009620394914864702 0.11495959335492903 chr12 133851895 2246162 0.016780950318260345 0.13744296979773257 chr13 115169878 869880 0.007553016596926499 0.09127428882272809 chr14 107349540 867433 0.008080453814706613 0.10231415033605674 chr15 102531392 1174355 0.011453614128246694 0.11336935614897155 chr16 90354753 853714 0.009448468084462584 0.10777397403443746 chr17 81195210 931931 0.011477659827470118 0.1135524766265436 chr18 78077248 749709 0.009602144276396628 0.17987426419904423 chr19 59128983 642362 0.01086374172882358 0.14765833601088793 chr20 63025520 683087 0.010838260437994006 0.10989492646439288 chr21 48129895 609189 0.012657185310709695 0.12041148293564337 chr22 51304566 506293 0.009868380915647937 0.10456555088167817 chrMT 16571 2438 0.14712449459899826 0.400297885743526 chrX 155270560 1620441 0.010436241100695458 0.11399787038305205 chrY 59373566 93625 0.0015768801894095429 0.049500579165289424