BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173876.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 = 3,148,502 number of mapped reads = 3,076,185 (97.7%) number of supplementary alignments = 309,072 (9.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,540,026 number of mapped paired reads (second in pair) = 1,536,159 number of mapped paired reads (both in pair) = 3,028,742 number of mapped paired reads (singletons) = 47,443 number of mapped bases = 362,277,965 bp number of sequenced bases = 362,045,555 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,307,532 duplication rate = 63.03% >>>>>>> Insert size mean insert size = 792,528.5389 std insert size = 8,484,253.8185 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 52.8229 >>>>>>> ACTG content number of A's = 109,541,786 bp (30.26%) number of C's = 70,342,414 bp (19.43%) number of T's = 109,265,195 bp (30.18%) number of G's = 72,892,237 bp (20.13%) number of N's = 3,923 bp (0%) GC percentage = 39.56% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 3,637,944 number of insertions = 36,916 mapped reads with insertion percentage = 1.16% number of deletions = 95,203 mapped reads with deletion percentage = 3.02% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.117X std coverageData = 1.8747X There is a 2.7% of reference with a coverageData >= 1X There is a 2.04% of reference with a coverageData >= 2X There is a 1.49% of reference with a coverageData >= 3X There is a 1.2% of reference with a coverageData >= 4X There is a 0.88% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.51% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% 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 0.03% 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 0.02% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 34097088 0.136798407415001 1.5337607720767221 chr2 243199373 33479099 0.13766112382205853 5.314226948003557 chr3 198022430 24937630 0.12593336017541043 1.0080559983915929 chr4 191154276 22584949 0.11815037294797423 1.0701100834539616 chr5 180915260 25287568 0.1397757602095036 1.0554139437330656 chr6 171115067 20511698 0.11987078846773908 0.9876212106659525 chr7 159138663 24167559 0.15186478599484024 1.6240371148015276 chr8 146364022 15852012 0.10830538668854017 1.0352844393305425 chr9 141213431 14008775 0.09920285132084922 0.9651855680672295 chr10 135534747 15089855 0.1113356931267227 1.9159865120207156 chr11 135006516 17972457 0.1331228857131607 1.0354120866808298 chr12 133851895 12481368 0.09324760026744484 0.8552561960892386 chr13 115169878 12300492 0.10680303056325197 0.9317767162053899 chr14 107349540 8483806 0.07902973780791236 0.7865447500172067 chr15 102531392 8068804 0.0786959373379033 0.776938846327318 chr16 90354753 14622429 0.16183353409200288 1.4788996435624868 chr17 81195210 8327962 0.10256715882624111 0.9743932221244783 chr18 78077248 5878239 0.07528747683319986 1.3236493362876303 chr19 59128983 6762388 0.11436672266120322 1.458338051321933 chr20 63025520 10865205 0.17239373828252427 1.1601142580634407 chr21 48129895 4618578 0.0959606913748721 0.8842101248835998 chr22 51304566 3038555 0.05922582017358845 0.6370499017973495 chrMT 16571 1142790 68.96324904954439 59.20894621173245 chrX 155270560 17130938 0.11032959499856251 0.9258816784567971 chrY 59373566 567721 0.009561847775826703 0.35256071699988234