BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617655.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 38,583,290 number of mapped reads = 37,756,200 (97.86%) number of supplementary alignments = 441,165 (1.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 19,062,343 number of mapped paired reads (second in pair) = 18,693,857 number of mapped paired reads (both in pair) = 37,273,744 number of mapped paired reads (singletons) = 482,456 number of mapped bases = 5,114,791,074 bp number of sequenced bases = 5,111,588,451 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,452,687 duplication rate = 20.95% >>>>>>> Insert size mean insert size = 76,923.484 std insert size = 2,670,854.0989 median insert size = 279 >>>>>>> Mapping quality mean mapping quality = 53.8156 >>>>>>> ACTG content number of A's = 1,486,890,418 bp (29.09%) number of C's = 968,952,361 bp (18.96%) number of T's = 1,524,477,243 bp (29.82%) number of G's = 1,131,063,322 bp (22.13%) number of N's = 205,107 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 58,464,547 number of insertions = 754,587 mapped reads with insertion percentage = 1.91% number of deletions = 1,758,435 mapped reads with deletion percentage = 4.5% homopolymer indels = 47.78% >>>>>>> Coverage mean coverageData = 1.6522X std coverageData = 14.6772X There is a 39.66% of reference with a coverageData >= 1X There is a 28.03% of reference with a coverageData >= 2X There is a 20.19% of reference with a coverageData >= 3X There is a 15.09% of reference with a coverageData >= 4X There is a 11.39% of reference with a coverageData >= 5X There is a 8.74% of reference with a coverageData >= 6X There is a 6.77% of reference with a coverageData >= 7X There is a 5.31% of reference with a coverageData >= 8X There is a 4.19% of reference with a coverageData >= 9X There is a 3.33% of reference with a coverageData >= 10X There is a 2.67% of reference with a coverageData >= 11X There is a 2.15% of reference with a coverageData >= 12X There is a 1.75% of reference with a coverageData >= 13X There is a 1.43% of reference with a coverageData >= 14X There is a 1.17% of reference with a coverageData >= 15X There is a 0.97% of reference with a coverageData >= 16X There is a 0.8% of reference with a coverageData >= 17X There is a 0.67% of reference with a coverageData >= 18X There is a 0.56% of reference with a coverageData >= 19X There is a 0.47% of reference with a coverageData >= 20X There is a 0.4% of reference with a coverageData >= 21X There is a 0.34% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 468347183 1.8790211278952038 14.815472979916754 chr2 243199373 503232063 2.0692161200596515 15.736842238452027 chr3 198022430 360194660 1.8189588926870557 3.6247492286418117 chr4 191154276 229006407 1.198018751095058 9.621509352617377 chr5 180915260 317400159 1.7544134143244743 3.3793903644090197 chr6 171115067 411845946 2.4068362489669015 11.640011726127534 chr7 159138663 295465800 1.856656292255013 16.37970131797574 chr8 146364022 263846313 1.8026719230221755 5.458343223672298 chr9 141213431 221582983 1.5691353253785045 32.07192251284898 chr10 135534747 263649189 1.9452516408947147 33.204072166345384 chr11 135006516 183654112 1.3603351707853863 15.71951275617757 chr12 133851895 222975583 1.665838074238695 5.914079627592565 chr13 115169878 177430732 1.54060015588451 3.285555205244043 chr14 107349540 152631391 1.4218169076458083 3.2663177368102665 chr15 102531392 146922658 1.4329529243102443 3.787931162510784 chr16 90354753 153935533 1.70367941794938 18.281961988434713 chr17 81195210 100500899 1.237768816658027 13.133351528070216 chr18 78077248 145045787 1.8577215605754958 23.5913021017317 chr19 59128983 63310434 1.0707174517106104 9.750014378020552 chr20 63025520 103850692 1.6477562105001275 4.291999577500977 chr21 48129895 64396842 1.337980105711845 5.847141127173739 chr22 51304566 47022224 0.9165309769894555 2.64785651395956 chrMT 16571 877661 52.96367147426226 34.32453970681781 chrX 155270560 159169776 1.0251123973533682 4.441598937646073 chrY 59373566 58496047 0.9852203756803154 19.58473560464874