BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716394.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 = 3,479,784 number of mapped reads = 3,190,159 (91.68%) number of supplementary alignments = 52,758 (1.52%) number of secondary alignments = 0 number of mapped bases = 251,370,881 bp number of sequenced bases = 251,260,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 205,546 duplication rate = 4.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6982 >>>>>>> ACTG content number of A's = 62,358,376 bp (24.82%) number of C's = 50,905,459 bp (20.26%) number of T's = 79,042,168 bp (31.46%) number of G's = 58,939,489 bp (23.46%) number of N's = 15,204 bp (0.01%) GC percentage = 43.72% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 2,078,681 number of insertions = 24,904 mapped reads with insertion percentage = 0.77% number of deletions = 62,996 mapped reads with deletion percentage = 1.94% homopolymer indels = 44.02% >>>>>>> Coverage mean coverageData = 0.0812X std coverageData = 0.8998X There is a 6.35% of reference with a coverageData >= 1X There is a 1.12% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 20640578 0.08281053791236091 1.510633103610545 chr2 243199373 20857494 0.08576294314706148 1.4112031520502681 chr3 198022430 16160863 0.08161127504596323 0.3629295581318602 chr4 191154276 16331354 0.08543546261031587 0.43503655453341983 chr5 180915260 15008043 0.0829562028100891 0.37098073557050765 chr6 171115067 14823352 0.0866279764832164 0.5265608212489477 chr7 159138663 13776118 0.08656675719337921 1.1113960329907089 chr8 146364022 13016864 0.08893486132814798 1.2340902817283257 chr9 141213431 10876621 0.07702256735055181 1.012106078104197 chr10 135534747 11189137 0.08255548667530992 0.9144293345555847 chr11 135006516 11255920 0.08337316104061229 0.7640680310964814 chr12 133851895 11207669 0.08373186647824447 0.377785579581309 chr13 115169878 7312953 0.06349709773939329 0.3066914003512427 chr14 107349540 7989436 0.07442450149297333 0.5681500138786174 chr15 102531392 7403079 0.07220304782363629 0.34266883350702504 chr16 90354753 7112288 0.07871515071265814 0.47231395251232505 chr17 81195210 7267295 0.0895039867499573 0.4387453743346676 chr18 78077248 7340647 0.0940177476542206 1.9247057180957536 chr19 59128983 5585989 0.09447125109525391 1.1124484935464318 chr20 63025520 5387367 0.0854791360705949 0.40685417962184095 chr21 48129895 3061877 0.06361694742945107 0.36918312939134074 chr22 51304566 2818651 0.05493957399425228 0.28985540098157475 chrMT 16571 61681 3.7222255747993485 2.9463764142239492 chrX 155270560 14179920 0.0913239444747285 0.6125352821636012 chrY 59373566 705685 0.01188550810641894 0.34341637609424824