BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173973.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 = 4,183,314 number of mapped reads = 4,108,021 (98.2%) number of supplementary alignments = 518,185 (12.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,053,577 number of mapped paired reads (second in pair) = 2,054,444 number of mapped paired reads (both in pair) = 4,060,572 number of mapped paired reads (singletons) = 47,449 number of mapped bases = 468,058,431 bp number of sequenced bases = 467,737,477 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,305,056 duplication rate = 65.24% >>>>>>> Insert size mean insert size = 976,394.9144 std insert size = 9,131,589.076 median insert size = 153 >>>>>>> Mapping quality mean mapping quality = 52.8089 >>>>>>> ACTG content number of A's = 138,611,150 bp (29.63%) number of C's = 94,122,247 bp (20.12%) number of T's = 137,404,383 bp (29.38%) number of G's = 97,596,311 bp (20.87%) number of N's = 3,386 bp (0%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 3,760,477 number of insertions = 48,574 mapped reads with insertion percentage = 1.14% number of deletions = 135,662 mapped reads with deletion percentage = 3.22% homopolymer indels = 41.6% >>>>>>> Coverage mean coverageData = 0.1512X std coverageData = 2.6578X There is a 3.19% of reference with a coverageData >= 1X There is a 2.4% of reference with a coverageData >= 2X There is a 1.79% of reference with a coverageData >= 3X There is a 1.46% of reference with a coverageData >= 4X There is a 1.1% of reference with a coverageData >= 5X There is a 0.92% of reference with a coverageData >= 6X There is a 0.7% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 41348227 0.1658901664281109 1.3941406252384825 chr2 243199373 42245585 0.17370762300443923 8.40595901000294 chr3 198022430 30782597 0.1554500517946376 1.1985625723682762 chr4 191154276 27811608 0.14549299436022034 1.33074384860877 chr5 180915260 29665867 0.16397658771294363 1.2519770291109926 chr6 171115067 28917001 0.16899155350241601 1.359547294911194 chr7 159138663 26883184 0.16892930663870162 1.418325161679237 chr8 146364022 23100121 0.1578264978260846 1.4410836213064844 chr9 141213431 20704112 0.1466157422377196 1.2966086349205241 chr10 135534747 22156192 0.1634724119859832 1.5365532308969108 chr11 135006516 23195900 0.17181318863157685 1.2869170309602052 chr12 133851895 20083832 0.1500451824010411 1.2074930118806972 chr13 115169878 14701202 0.12764797753801563 1.0936362625687157 chr14 107349540 15081319 0.1404879704188765 1.151543496915649 chr15 102531392 15638017 0.15251930842799832 1.2177962437155183 chr16 90354753 13845891 0.15323921033794427 1.2485720851742161 chr17 81195210 15054010 0.18540514889979348 1.3211911453077692 chr18 78077248 10233923 0.13107433038623492 1.3880456546267137 chr19 59128983 9498751 0.1606445860907163 1.2558121989205644 chr20 63025520 10052863 0.15950464192917407 1.2374793225076395 chr21 48129895 6003205 0.12472923533284251 1.2088227578339832 chr22 51304566 7099861 0.13838653269184656 1.241021022547999 chrMT 16571 530163 31.993422243678715 29.218007948772918 chrX 155270560 10734277 0.06913272548253835 0.7968710371380123 chrY 59373566 2690723 0.0453185345141641 0.8163045789720788