BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354866.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 = 17,775,892 number of mapped reads = 17,505,977 (98.48%) number of supplementary alignments = 609,666 (3.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,760,206 number of mapped paired reads (second in pair) = 8,745,771 number of mapped paired reads (both in pair) = 17,472,148 number of mapped paired reads (singletons) = 33,829 number of mapped bases = 2,266,467,337 bp number of sequenced bases = 2,265,326,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,113,065 duplication rate = 52.12% >>>>>>> Insert size mean insert size = 301,280.0903 std insert size = 6,266,653.9342 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.8384 >>>>>>> ACTG content number of A's = 637,244,153 bp (28.13%) number of C's = 478,606,048 bp (21.13%) number of T's = 647,941,619 bp (28.6%) number of G's = 501,499,156 bp (22.14%) number of N's = 35,562 bp (0%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 13,532,655 number of insertions = 381,557 mapped reads with insertion percentage = 2.04% number of deletions = 406,521 mapped reads with deletion percentage = 2.22% homopolymer indels = 45.2% >>>>>>> Coverage mean coverageData = 0.7321X std coverageData = 28.5246X There is a 25.15% of reference with a coverageData >= 1X There is a 18.19% of reference with a coverageData >= 2X There is a 9.36% of reference with a coverageData >= 3X There is a 6.79% of reference with a coverageData >= 4X There is a 3.43% of reference with a coverageData >= 5X There is a 2.52% of reference with a coverageData >= 6X There is a 1.28% of reference with a coverageData >= 7X There is a 0.95% of reference with a coverageData >= 8X There is a 0.49% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 185553949 0.7444472886589117 19.08595943819898 chr2 243199373 211630755 0.8701944926478079 95.26336910304772 chr3 198022430 147282197 0.7437652239698301 1.9054108589380911 chr4 191154276 150040955 0.7849207359609366 9.161442923577848 chr5 180915260 133616393 0.7385578916891808 1.6512231096281773 chr6 171115067 128182947 0.7491038004268789 2.9703314380124715 chr7 159138663 123506422 0.7760931232657146 22.893461701188528 chr8 146364022 111125809 0.7592426573246258 5.669457085748192 chr9 141213431 95601526 0.6770002351971747 11.006489269348844 chr10 135534747 124727343 0.9202610087876579 22.302573518891318 chr11 135006516 105088807 0.7783980367288347 3.653369601171882 chr12 133851895 100267765 0.749094848451716 1.6676765056830432 chr13 115169878 69436573 0.6029056746938639 1.4733433482017886 chr14 107349540 69273480 0.6453076557198103 2.5703616384910646 chr15 102531392 63563346 0.6199403398327021 1.496654800667062 chr16 90354753 73953882 0.8184835832598646 4.511661506992394 chr17 81195210 64637171 0.7960712337587402 4.579818982172724 chr18 78077248 62366888 0.79878440387653 8.878057774258554 chr19 59128983 48265713 0.8162784230535471 9.875400481804688 chr20 63025520 47508795 0.7538025073018041 3.3856798115513564 chr21 48129895 32459951 0.6744238897674719 5.008976077014679 chr22 51304566 30028469 0.5852981779438501 2.616172692338872 chrMT 16571 2673398 161.3299137046648 33.64396290082267 chrX 155270560 61123902 0.39366060121120194 1.6723308834198949 chrY 59373566 24550901 0.41349884559738254 11.262302338123222