BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525213.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 = 1,137,382 number of mapped reads = 1,015,662 (89.3%) number of supplementary alignments = 3,315 (0.29%) number of secondary alignments = 0 number of mapped bases = 60,529,187 bp number of sequenced bases = 60,509,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,034 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2094 >>>>>>> ACTG content number of A's = 15,969,174 bp (26.39%) number of C's = 12,034,122 bp (19.89%) number of T's = 18,575,262 bp (30.7%) number of G's = 13,929,662 bp (23.02%) number of N's = 1,351 bp (0%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 300,391 number of insertions = 4,490 mapped reads with insertion percentage = 0.44% number of deletions = 12,279 mapped reads with deletion percentage = 1.2% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.2148X There is a 1.82% of reference with a coverageData >= 1X There is a 0.09% 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 5886875 0.02361829622081463 0.3982125861198702 chr2 243199373 4737525 0.01948000499162471 0.22514556366680755 chr3 198022430 5181469 0.02616607118698624 0.1722157567117634 chr4 191154276 3464987 0.018126651794072343 0.1455350848621601 chr5 180915260 2953384 0.016324681511111886 0.13408121510263984 chr6 171115067 3974273 0.023225733827401653 0.17082912921609664 chr7 159138663 4521521 0.028412460647605164 0.376906236135729 chr8 146364022 3428327 0.023423290458634706 0.19383822972246748 chr9 141213431 1831060 0.012966613636064122 0.14630619198318265 chr10 135534747 3297568 0.024330056114687696 0.24580474839102112 chr11 135006516 2824798 0.020923419725904193 0.17178441634249975 chr12 133851895 2665165 0.01991129823003253 0.14950098929907726 chr13 115169878 2253170 0.01956388284096298 0.14664630837438225 chr14 107349540 1745636 0.0162612340956468 0.13759761225323264 chr15 102531392 1728728 0.016860475277659354 0.13667799894275232 chr16 90354753 1608343 0.017800314278984306 0.1538095436625776 chr17 81195210 1129273 0.013908123397919655 0.12994396500218264 chr18 78077248 1271188 0.016281157860481968 0.26989454694685383 chr19 59128983 1094428 0.018509163264316588 0.27479995587317807 chr20 63025520 1112865 0.017657371172820152 0.14253798149949998 chr21 48129895 814282 0.01691842460907093 0.14226562839122422 chr22 51304566 504615 0.009835674275073295 0.10394308179397913 chrMT 16571 29809 1.7988654879005492 1.694279153998717 chrX 155270560 2303000 0.014832174238310212 0.13717960292063336 chrY 59373566 166898 0.0028109815738539268 0.0927824705800185