BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156410.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,270,332 number of mapped reads = 2,225,315 (98.02%) number of supplementary alignments = 300,161 (13.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,112,674 number of mapped paired reads (second in pair) = 1,112,641 number of mapped paired reads (both in pair) = 2,198,986 number of mapped paired reads (singletons) = 26,329 number of mapped bases = 250,168,309 bp number of sequenced bases = 249,999,060 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,679,140 duplication rate = 59.97% >>>>>>> Insert size mean insert size = 900,021.8813 std insert size = 8,658,779.1856 median insert size = 141 >>>>>>> Mapping quality mean mapping quality = 52.671 >>>>>>> ACTG content number of A's = 75,145,434 bp (30.06%) number of C's = 49,308,826 bp (19.72%) number of T's = 74,524,050 bp (29.81%) number of G's = 51,018,729 bp (20.41%) number of N's = 2,021 bp (0%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 2,058,876 number of insertions = 27,963 mapped reads with insertion percentage = 1.21% number of deletions = 70,542 mapped reads with deletion percentage = 3.1% homopolymer indels = 41.16% >>>>>>> Coverage mean coverageData = 0.0808X std coverageData = 1.5918X There is a 2.04% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 20066520 0.08050740222629174 1.0107129637269834 chr2 243199373 22945692 0.09434930574430388 4.790103380630689 chr3 198022430 16676849 0.08421696976448577 0.8212063747547308 chr4 191154276 16256506 0.0850439045370871 0.9354278630900792 chr5 180915260 15213655 0.08409271279824598 0.8244968406178752 chr6 171115067 14627251 0.08548195817262544 0.8671172508688713 chr7 159138663 14636182 0.09197125151164554 1.0234210782212012 chr8 146364022 12380410 0.08458642930706017 1.0723917692647293 chr9 141213431 10490918 0.07429121950871656 0.8657841770606863 chr10 135534747 13218200 0.09752628231932288 1.1381300789886135 chr11 135006516 11916036 0.08826267318830744 0.853912106341529 chr12 133851895 12185575 0.09103774735501503 0.8679338837786846 chr13 115169878 8043716 0.06984218564510418 0.7556349919962333 chr14 107349540 7585891 0.07066533307921022 0.7516280958076065 chr15 102531392 7248483 0.07069525594658853 0.7474904333493038 chr16 90354753 7466287 0.08263302983076054 0.8758660435201744 chr17 81195210 6451843 0.0794608819904524 0.792804317488985 chr18 78077248 6884578 0.08817649413053083 1.047414392366195 chr19 59128983 4713518 0.07971586455325978 0.8407579309873947 chr20 63025520 5547238 0.08801574346391747 0.8486814816445424 chr21 48129895 3565649 0.07408387240404327 0.872244761554605 chr22 51304566 3118795 0.060789813522640464 0.7194879060871765 chrMT 16571 519709 31.36256110071812 23.90501414991259 chrX 155270560 6548598 0.042175400153126257 0.5806092299523884 chrY 59373566 1860210 0.0313306093152633 0.6180875351770533