BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354858.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 = 43,532,500 number of mapped reads = 42,769,440 (98.25%) number of supplementary alignments = 842,148 (1.93%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,414,514 number of mapped paired reads (second in pair) = 21,354,926 number of mapped paired reads (both in pair) = 42,644,708 number of mapped paired reads (singletons) = 124,732 number of mapped bases = 5,854,141,004 bp number of sequenced bases = 5,850,906,729 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,860,803 duplication rate = 57.16% >>>>>>> Insert size mean insert size = 155,838.8086 std insert size = 4,443,238.4648 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 53.9088 >>>>>>> ACTG content number of A's = 1,639,153,578 bp (28.02%) number of C's = 1,265,172,087 bp (21.62%) number of T's = 1,664,813,426 bp (28.45%) number of G's = 1,281,735,384 bp (21.91%) number of N's = 32,254 bp (0%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 43,173,488 number of insertions = 1,077,038 mapped reads with insertion percentage = 2.3% number of deletions = 1,048,870 mapped reads with deletion percentage = 2.31% homopolymer indels = 41.88% >>>>>>> Coverage mean coverageData = 1.8911X std coverageData = 39.6993X There is a 49.66% of reference with a coverageData >= 1X There is a 38.12% of reference with a coverageData >= 2X There is a 25.54% of reference with a coverageData >= 3X There is a 19.19% of reference with a coverageData >= 4X There is a 12.59% of reference with a coverageData >= 5X There is a 9.41% of reference with a coverageData >= 6X There is a 6.13% of reference with a coverageData >= 7X There is a 4.56% of reference with a coverageData >= 8X There is a 2.97% of reference with a coverageData >= 9X There is a 2.21% of reference with a coverageData >= 10X There is a 1.45% of reference with a coverageData >= 11X There is a 1.08% of reference with a coverageData >= 12X There is a 0.72% of reference with a coverageData >= 13X There is a 0.54% of reference with a coverageData >= 14X There is a 0.37% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.21% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% 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 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 483425358 1.9395151597235138 57.72299311772332 chr2 243199373 508865462 2.092379826982531 90.99877021950404 chr3 198022430 372377659 1.8804822211302024 3.9271739440595934 chr4 191154276 396614701 2.074840852631515 44.17550434398936 chr5 180915260 342025540 1.8905289691980653 3.0294996302644153 chr6 171115067 321839010 1.8808338484886313 8.22995279512972 chr7 159138663 313795141 1.971834720013954 30.079107279209342 chr8 146364022 281611409 1.9240480355206417 6.88412604282225 chr9 141213431 250136455 1.7713361486132293 33.33621851150305 chr10 135534747 344193880 2.539525011988254 84.80133571987528 chr11 135006516 269804506 1.9984554375138457 9.874142189763973 chr12 133851895 255914253 1.9119210303298284 2.969562370768089 chr13 115169878 172615266 1.4987883029623423 2.523880113495141 chr14 107349540 175345861 1.6334104552287787 3.762090205873838 chr15 102531392 164157583 1.6010470529845142 2.6297448469878875 chr16 90354753 196424239 2.1739225937566338 15.301559533317679 chr17 81195210 173371692 2.135245318042776 13.00793136095444 chr18 78077248 159265245 2.0398419396134453 29.25033492839373 chr19 59128983 129147088 2.1841587906221895 29.810404099613383 chr20 63025520 125074911 1.984512162692192 13.610855925380603 chr21 48129895 84870707 1.7633677987454575 21.233995462612004 chr22 51304566 80168534 1.5626003736197671 5.512664205908241 chrMT 16571 11956367 721.5235652646189 168.84748696656553 chrX 155270560 155231088 0.9997457856788821 3.8755138567434426 chrY 59373566 85909049 1.4469241918196392 49.344731924065414