BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354880.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 19,912,198 number of mapped reads = 19,771,418 (99.29%) number of supplementary alignments = 446,248 (2.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,895,855 number of mapped paired reads (second in pair) = 9,875,563 number of mapped paired reads (both in pair) = 19,728,188 number of mapped paired reads (singletons) = 43,230 number of mapped bases = 2,637,755,252 bp number of sequenced bases = 2,636,190,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,126,359 duplication rate = 33.68% >>>>>>> Insert size mean insert size = 201,368.4055 std insert size = 5,132,622.0169 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 54.0293 >>>>>>> ACTG content number of A's = 756,558,841 bp (28.7%) number of C's = 551,242,097 bp (20.91%) number of T's = 765,991,443 bp (29.06%) number of G's = 562,385,426 bp (21.33%) number of N's = 12,419 bp (0%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 20,576,657 number of insertions = 531,977 mapped reads with insertion percentage = 2.5% number of deletions = 549,190 mapped reads with deletion percentage = 2.64% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.8521X std coverageData = 19.9691X There is a 35.9% of reference with a coverageData >= 1X There is a 22.44% of reference with a coverageData >= 2X There is a 9.68% of reference with a coverageData >= 3X There is a 6% of reference with a coverageData >= 4X There is a 2.59% of reference with a coverageData >= 5X There is a 1.59% of reference with a coverageData >= 6X There is a 0.71% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% 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 0.02% 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 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 213867044 0.8580401651236006 23.112702718367114 chr2 243199373 238814541 0.9819702166748596 58.02574140166978 chr3 198022430 172306473 0.8701361406382095 1.8306902619960697 chr4 191154276 181744181 0.9507722495310542 14.696065773394082 chr5 180915260 157651334 0.8714098191606391 1.5516310962200808 chr6 171115067 150093020 0.8771467213930378 3.4064353187124787 chr7 159138663 143287944 0.9003968067772443 12.469585068189629 chr8 146364022 129585870 0.8853669653871632 3.6343361826392786 chr9 141213431 112216993 0.7946623221696242 12.83229010128943 chr10 135534747 147581448 1.0888827497497744 30.823992757612295 chr11 135006516 119326444 0.8838569243576362 4.432807653595163 chr12 133851895 116692555 0.8718035333007426 1.5520410971589824 chr13 115169878 81764366 0.7099457550871071 1.3466508730145972 chr14 107349540 79477517 0.7403619708104944 3.2647596418558 chr15 102531392 74081628 0.7225263068699974 1.3548776010310715 chr16 90354753 81601054 0.9031185553680834 5.719537771521053 chr17 81195210 72600235 0.8941443097443802 4.976892299661051 chr18 78077248 72032454 0.9225793152955392 10.560805538174344 chr19 59128983 52542809 0.8886134402142516 11.798329220066947 chr20 63025520 54763407 0.8689084516875069 4.732693535732917 chr21 48129895 37116670 0.7711770407976165 7.2728536983510725 chr22 51304566 31515525 0.6142830445149853 2.4444542401220675 chrMT 16571 12497946 754.2059018767727 178.14435848344823 chrX 155270560 70786366 0.45589045341241763 1.7797660920420026 chrY 59373566 33807428 0.5694020130103016 17.520586847659455