BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173975.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 = 4,162,458 number of mapped reads = 4,071,818 (97.82%) number of supplementary alignments = 510,768 (12.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,038,214 number of mapped paired reads (second in pair) = 2,033,604 number of mapped paired reads (both in pair) = 4,016,370 number of mapped paired reads (singletons) = 55,448 number of mapped bases = 459,685,813 bp number of sequenced bases = 459,355,908 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,262,771 duplication rate = 64.73% >>>>>>> Insert size mean insert size = 1,022,602.5932 std insert size = 9,200,106.6556 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 52.6191 >>>>>>> ACTG content number of A's = 137,743,644 bp (29.99%) number of C's = 90,909,917 bp (19.79%) number of T's = 136,482,040 bp (29.71%) number of G's = 94,216,697 bp (20.51%) number of N's = 3,610 bp (0%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 3,923,457 number of insertions = 49,712 mapped reads with insertion percentage = 1.17% number of deletions = 136,453 mapped reads with deletion percentage = 3.27% homopolymer indels = 40.84% >>>>>>> Coverage mean coverageData = 0.1485X std coverageData = 2.6685X There is a 3.14% of reference with a coverageData >= 1X There is a 2.35% of reference with a coverageData >= 2X There is a 1.76% of reference with a coverageData >= 3X There is a 1.42% of reference with a coverageData >= 4X There is a 1.07% of reference with a coverageData >= 5X There is a 0.9% of reference with a coverageData >= 6X There is a 0.68% of reference with a coverageData >= 7X There is a 0.59% of reference with a coverageData >= 8X There is a 0.44% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.3% 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 0.19% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.13% 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 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% 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 0.01% 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 36854252 0.14786022137934815 1.4299870256689826 chr2 243199373 42610730 0.17520904546082033 8.311736707470521 chr3 198022430 32094275 0.16207393778573467 1.2374450412170261 chr4 191154276 32079834 0.16782169183597023 1.5295260464165323 chr5 180915260 28687821 0.15857048764156212 1.2223547151338485 chr6 171115067 27300661 0.1595456290240064 1.3414854026187084 chr7 159138663 25095913 0.15769840293304463 1.4790874871138688 chr8 146364022 23755015 0.16230091709286315 1.7169342623695785 chr9 141213431 19684258 0.13939366716470475 1.3849526775350758 chr10 135534747 22368122 0.1650360700492546 1.8238194569383237 chr11 135006516 20573627 0.15238988168541434 1.2021838809848355 chr12 133851895 20968507 0.1566545397059937 1.2518787154318836 chr13 115169878 14762609 0.12818116382827113 1.1003483190214747 chr14 107349540 14368241 0.1338453895563968 1.125828588020832 chr15 102531392 12927130 0.1260797278554455 1.1050517208168644 chr16 90354753 13264215 0.14680151911875627 1.3339068570835377 chr17 81195210 12396136 0.15267077947085794 1.2426524831788945 chr18 78077248 12745324 0.16323992362025874 1.7715950620057872 chr19 59128983 8403878 0.14212789690632766 1.260243144586999 chr20 63025520 9871997 0.15663491550724215 1.2388773769392114 chr21 48129895 6270129 0.1302751439619804 1.3688186015448813 chr22 51304566 5592974 0.109015131323789 1.204014052456332 chrMT 16571 541067 32.65143926136021 29.48894832138525 chrX 155270560 12757276 0.08216158942171652 0.8731229953654721 chrY 59373566 3711822 0.06251640671203748 0.9989345291159314