BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354865.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 163,625,886 number of mapped reads = 156,904,229 (95.89%) number of supplementary alignments = 6,671,641 (4.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 78,556,779 number of mapped paired reads (second in pair) = 78,347,450 number of mapped paired reads (both in pair) = 156,531,170 number of mapped paired reads (singletons) = 373,059 number of mapped bases = 18,542,014,077 bp number of sequenced bases = 18,533,847,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,919,902 duplication rate = 85.75% >>>>>>> Insert size mean insert size = 469,510.1927 std insert size = 7,910,704.8044 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 53.5523 >>>>>>> ACTG content number of A's = 5,131,776,858 bp (27.69%) number of C's = 3,901,444,085 bp (21.05%) number of T's = 5,169,535,003 bp (27.89%) number of G's = 4,330,692,461 bp (23.37%) number of N's = 399,108 bp (0%) GC percentage = 44.42% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 108,546,256 number of insertions = 2,963,941 mapped reads with insertion percentage = 1.79% number of deletions = 3,205,876 mapped reads with deletion percentage = 1.97% homopolymer indels = 43.33% >>>>>>> Coverage mean coverageData = 5.9896X std coverageData = 360.1994X There is a 44.65% of reference with a coverageData >= 1X There is a 43.1% of reference with a coverageData >= 2X There is a 39.96% of reference with a coverageData >= 3X There is a 38.36% of reference with a coverageData >= 4X There is a 34.95% of reference with a coverageData >= 5X There is a 33.36% of reference with a coverageData >= 6X There is a 29.83% of reference with a coverageData >= 7X There is a 28.48% of reference with a coverageData >= 8X There is a 25.1% of reference with a coverageData >= 9X There is a 23.99% of reference with a coverageData >= 10X There is a 20.9% of reference with a coverageData >= 11X There is a 20.01% of reference with a coverageData >= 12X There is a 17.28% of reference with a coverageData >= 13X There is a 16.56% of reference with a coverageData >= 14X There is a 14.19% of reference with a coverageData >= 15X There is a 13.63% of reference with a coverageData >= 16X There is a 11.6% of reference with a coverageData >= 17X There is a 11.14% of reference with a coverageData >= 18X There is a 9.42% of reference with a coverageData >= 19X There is a 9.05% of reference with a coverageData >= 20X There is a 7.61% of reference with a coverageData >= 21X There is a 7.3% of reference with a coverageData >= 22X There is a 6.1% of reference with a coverageData >= 23X There is a 5.85% of reference with a coverageData >= 24X There is a 4.86% of reference with a coverageData >= 25X There is a 4.65% of reference with a coverageData >= 26X There is a 3.85% of reference with a coverageData >= 27X There is a 3.68% of reference with a coverageData >= 28X There is a 3.04% of reference with a coverageData >= 29X There is a 2.89% of reference with a coverageData >= 30X There is a 2.39% of reference with a coverageData >= 31X There is a 2.27% of reference with a coverageData >= 32X There is a 1.88% of reference with a coverageData >= 33X There is a 1.78% of reference with a coverageData >= 34X There is a 1.47% of reference with a coverageData >= 35X There is a 1.4% of reference with a coverageData >= 36X There is a 1.15% of reference with a coverageData >= 37X There is a 1.09% of reference with a coverageData >= 38X There is a 0.91% of reference with a coverageData >= 39X There is a 0.86% of reference with a coverageData >= 40X There is a 0.71% of reference with a coverageData >= 41X There is a 0.68% of reference with a coverageData >= 42X There is a 0.56% of reference with a coverageData >= 43X There is a 0.53% of reference with a coverageData >= 44X There is a 0.45% of reference with a coverageData >= 45X There is a 0.42% of reference with a coverageData >= 46X There is a 0.36% of reference with a coverageData >= 47X There is a 0.34% of reference with a coverageData >= 48X There is a 0.29% of reference with a coverageData >= 49X There is a 0.27% of reference with a coverageData >= 50X There is a 0.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1503099862 6.030475895985832 171.71183926530506 chr2 243199373 1852246551 7.616164993155636 1251.7861909970268 chr3 198022430 1198114205 6.0503964374136805 16.223736285799458 chr4 191154276 1229771657 6.433398628236807 63.41180879048414 chr5 180915260 1082439108 5.983127725101796 10.263745925263043 chr6 171115067 1062586777 6.209779159891279 25.301934216507778 chr7 159138663 1016921714 6.390161226879228 141.27099104701603 chr8 146364022 916954957 6.264893137467895 21.376074046013766 chr9 141213431 784567958 5.555901817866036 82.30519854536591 chr10 135534747 1032633967 7.618961114082428 199.46203904324437 chr11 135006516 848653682 6.2860201651304 33.45917600721058 chr12 133851895 823491025 6.152255259441788 10.456178629275255 chr13 115169878 572927657 4.974631101024523 8.783748005093383 chr14 107349540 557900614 5.197047085623282 46.26715652130434 chr15 102531392 519443128 5.066186246647271 8.758107928710533 chr16 90354753 456066960 5.047514877274912 38.178694100111315 chr17 81195210 515143717 6.344508709319182 37.311766281044775 chr18 78077248 512029149 6.557981513385307 81.08740723273016 chr19 59128983 367692394 6.218479928870077 83.69896523842257 chr20 63025520 397205843 6.302301718415016 22.835291864893797 chr21 48129895 259526005 5.392199692104045 39.511214365524275 chr22 51304566 227566592 4.435601150977479 19.17702576266334 chrMT 16571 87060879 5253.809607145013 1004.8075577182691 chrX 155270560 511174784 3.29215521603065 15.39731562643629 chrY 59373566 206794892 3.4829454575795564 86.66190403760082