BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173894.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 = 1,622,126 number of mapped reads = 1,581,819 (97.52%) number of supplementary alignments = 151,433 (9.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 791,881 number of mapped paired reads (second in pair) = 789,938 number of mapped paired reads (both in pair) = 1,557,558 number of mapped paired reads (singletons) = 24,261 number of mapped bases = 187,143,501 bp number of sequenced bases = 187,031,852 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,147,063 duplication rate = 60.88% >>>>>>> Insert size mean insert size = 919,873.8873 std insert size = 8,861,162.0763 median insert size = 190 >>>>>>> Mapping quality mean mapping quality = 53.1817 >>>>>>> ACTG content number of A's = 56,960,565 bp (30.46%) number of C's = 36,036,654 bp (19.27%) number of T's = 56,754,715 bp (30.34%) number of G's = 37,277,660 bp (19.93%) number of N's = 2,258 bp (0%) GC percentage = 39.2% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,898,194 number of insertions = 20,942 mapped reads with insertion percentage = 1.28% number of deletions = 47,772 mapped reads with deletion percentage = 2.95% homopolymer indels = 42.33% >>>>>>> Coverage mean coverageData = 0.0605X std coverageData = 1.0073X There is a 1.5% of reference with a coverageData >= 1X There is a 1.1% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 14565497 0.058437154305023775 0.762881477077041 chr2 243199373 16744822 0.06885224165442236 2.570901828343084 chr3 198022430 12628895 0.06377507335911392 0.7041156109296715 chr4 191154276 13414140 0.07017441765205398 0.8081985086213493 chr5 180915260 11721339 0.06478911176425914 0.7003644265104861 chr6 171115067 11412372 0.0666941386289496 0.7318895003471725 chr7 159138663 10671303 0.06705663349704025 0.7923206852037488 chr8 146364022 9680540 0.0661401611387804 0.8788963864383159 chr9 141213431 8453789 0.059865332498011466 0.7780033163559416 chr10 135534747 8878834 0.06550965118929981 0.932907762344977 chr11 135006516 8749988 0.06481159768614428 0.701492888156791 chr12 133851895 8828071 0.06595402328820223 0.702007703644693 chr13 115169878 6306032 0.05475417799782683 0.6522092031439481 chr14 107349540 5570489 0.051891130600093864 0.6291626785113099 chr15 102531392 5091750 0.049660400592240084 0.5989632887995828 chr16 90354753 5463018 0.06046187741778233 0.722553932712437 chr17 81195210 4615614 0.05684589029328208 0.6502833847407334 chr18 78077248 5346826 0.06848123028106728 0.93186425248866 chr19 59128983 3182102 0.05381628160254338 0.656263296775786 chr20 63025520 3900815 0.06189262698665556 0.6635097055164018 chr21 48129895 2694401 0.055981859091942754 0.7161830890331846 chr22 51304566 2242241 0.043704511602339645 0.5728023004719623 chrMT 16571 293802 17.729889566109467 17.021258970169377 chrX 155270560 5244226 0.033774760650054976 0.49716066792141844 chrY 59373566 1442595 0.024296923651175004 0.5102942441493243