BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525154.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 = 2,610,705 number of mapped reads = 905,375 (34.68%) number of supplementary alignments = 2,863 (0.11%) number of secondary alignments = 0 number of mapped bases = 53,299,828 bp number of sequenced bases = 53,283,360 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,592 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1485 >>>>>>> ACTG content number of A's = 13,761,124 bp (25.83%) number of C's = 9,241,131 bp (17.34%) number of T's = 16,788,169 bp (31.51%) number of G's = 13,491,665 bp (25.32%) number of N's = 1,271 bp (0%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 267,236 number of insertions = 3,931 mapped reads with insertion percentage = 0.43% number of deletions = 10,400 mapped reads with deletion percentage = 1.14% homopolymer indels = 44.06% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 0.1814X There is a 1.6% of reference with a coverageData >= 1X There is a 0.08% 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 4541750 0.01822161959628578 0.26101915468657205 chr2 243199373 4637100 0.019067072183611262 0.24189183700035705 chr3 198022430 4157351 0.02099434392356462 0.15283267359977712 chr4 191154276 2894235 0.015140833156146609 0.134091909840993 chr5 180915260 2557330 0.014135512946779614 0.12489738933022275 chr6 171115067 3341274 0.01952647454475765 0.1576379311721134 chr7 159138663 4057754 0.0254982285480179 0.3108240939187809 chr8 146364022 2727426 0.018634538479681845 0.16281541939460378 chr9 141213431 1905392 0.013492994161440635 0.14048470403605962 chr10 135534747 2621026 0.0193384062612372 0.18471940380435925 chr11 135006516 2623760 0.01943432122935459 0.16449637700269046 chr12 133851895 2587068 0.019327839923372024 0.14674630177671324 chr13 115169878 1240586 0.010771792256305073 0.10958488485335867 chr14 107349540 2498566 0.023275050829281618 0.1637644253802696 chr15 102531392 1102864 0.010756354502628815 0.11080543718097287 chr16 90354753 1414905 0.015659441844747227 0.1406992544390816 chr17 81195210 1041571 0.012827985788816852 0.1236661498837594 chr18 78077248 662254 0.008482035637321644 0.2238897379162895 chr19 59128983 1072196 0.018133171679952622 0.20835221256727982 chr20 63025520 1000231 0.015870253827338515 0.1338239836689727 chr21 48129895 722151 0.015004208922541801 0.1337417244840549 chr22 51304566 469059 0.00914263654427951 0.10090135164025014 chrMT 16571 80914 4.882867660370527 3.2370590102722856 chrX 155270560 3199401 0.020605329175086378 0.1565471084861183 chrY 59373566 143664 0.002419662649199814 0.07390436653354844