BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524662.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,193,954 number of mapped reads = 1,102,078 (92.3%) number of supplementary alignments = 4,957 (0.42%) number of secondary alignments = 0 number of mapped bases = 65,120,747 bp number of sequenced bases = 65,100,755 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,985 duplication rate = 2.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7079 >>>>>>> ACTG content number of A's = 16,890,459 bp (25.95%) number of C's = 12,744,813 bp (19.58%) number of T's = 20,313,099 bp (31.2%) number of G's = 15,143,101 bp (23.26%) number of N's = 9,283 bp (0.01%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 327,904 number of insertions = 4,530 mapped reads with insertion percentage = 0.41% number of deletions = 12,531 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.98% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.213X There is a 1.93% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% 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 5246300 0.021048292593822664 0.3537951874877066 chr2 243199373 5478506 0.022526809721668154 0.27788581630451414 chr3 198022430 4339585 0.021914613410208127 0.15792567781886818 chr4 191154276 4218211 0.022067050176790184 0.17181984593652092 chr5 180915260 3978177 0.02198917327371942 0.15805710030171496 chr6 171115067 3548473 0.020737349797490364 0.16778088674172445 chr7 159138663 3600940 0.022627687905107007 0.2613426766542658 chr8 146364022 3345562 0.02285781679325538 0.2244403087782263 chr9 141213431 2718183 0.019248756869309408 0.17967231781782128 chr10 135534747 3157505 0.023296645840937012 0.21982528979718663 chr11 135006516 2958704 0.02191526814898327 0.18958396572299555 chr12 133851895 2915801 0.021783785728248375 0.1586182120164239 chr13 115169878 2048675 0.01778828835782912 0.14419109384782355 chr14 107349540 1994166 0.018576381417190983 0.15172335562780062 chr15 102531392 1868168 0.018220449011362296 0.14383059538068507 chr16 90354753 1913788 0.02118082266242264 0.1645119085035194 chr17 81195210 1780562 0.02192939706664962 0.16502631596558456 chr18 78077248 1763143 0.022582033116741 0.3144378361734566 chr19 59128983 1351313 0.022853648607485774 0.26595177912337076 chr20 63025520 1398048 0.022182252522470264 0.16195700390766168 chr21 48129895 854702 0.017758235292223264 0.1539232474522857 chr22 51304566 766433 0.014938884776844229 0.13049601550916273 chrMT 16571 42984 2.5939291533401727 2.2135810718458324 chrX 155270560 3618445 0.023304127968624574 0.1733553240031854 chrY 59373566 214373 0.0036105798327828245 0.12560814410656282