BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524669.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 = 2,291,707 number of mapped reads = 2,114,427 (92.26%) number of supplementary alignments = 9,032 (0.39%) number of secondary alignments = 0 number of mapped bases = 124,688,891 bp number of sequenced bases = 124,651,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,246 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6783 >>>>>>> ACTG content number of A's = 33,323,393 bp (26.73%) number of C's = 23,333,947 bp (18.72%) number of T's = 37,889,709 bp (30.4%) number of G's = 30,087,311 bp (24.14%) number of N's = 17,232 bp (0.01%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 621,555 number of insertions = 10,588 mapped reads with insertion percentage = 0.5% number of deletions = 23,383 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.13% >>>>>>> Coverage mean coverageData = 0.0403X std coverageData = 0.3629X There is a 3.53% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9879761 0.03963785911690868 0.6630980120587854 chr2 243199373 10360092 0.042599172325991155 0.5039976458825363 chr3 198022430 8494653 0.04289742833677983 0.23425920663461292 chr4 191154276 8319291 0.04352134398500194 0.2661540534685003 chr5 180915260 7620776 0.042123456031293326 0.23046977206351912 chr6 171115067 7170589 0.04190507081413234 0.26758874923618436 chr7 159138663 6890727 0.04330014385002091 0.4371991196264707 chr8 146364022 6321069 0.04318731416112629 0.3950479740286094 chr9 141213431 5173534 0.03663627434985274 0.2950832853867907 chr10 135534747 5948953 0.043892456596388525 0.3632887922917092 chr11 135006516 5576092 0.04130239165641457 0.30833109453515906 chr12 133851895 5693733 0.04253755989035493 0.2317013317021754 chr13 115169878 3942542 0.03423240580319101 0.20855711626950243 chr14 107349540 3801735 0.03541454392818078 0.2193814195602547 chr15 102531392 3517363 0.03430523014844078 0.20901843637195486 chr16 90354753 3624163 0.040110374713768514 0.24643592453797863 chr17 81195210 3397056 0.04183813306228286 0.244781261982387 chr18 78077248 3291073 0.04215149847494625 0.5591673634769779 chr19 59128983 2580546 0.04364265828823743 0.5040333211892106 chr20 63025520 2624651 0.04164425775463654 0.23032777876879243 chr21 48129895 1632901 0.03392695953315502 0.24447618641139507 chr22 51304566 1453795 0.028336561700960494 0.18647989087362374 chrMT 16571 18572 1.120753122925593 1.2744703596298883 chrX 155270560 6956330 0.044801345470770505 0.26586616677951863 chrY 59373566 398894 0.006718376996254528 0.22486227208386816