BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524905.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 = 1,110,972 number of mapped reads = 1,027,716 (92.51%) number of supplementary alignments = 3,913 (0.35%) number of secondary alignments = 0 number of mapped bases = 59,696,525 bp number of sequenced bases = 59,677,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,187 duplication rate = 3.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8639 >>>>>>> ACTG content number of A's = 14,587,276 bp (24.44%) number of C's = 10,637,243 bp (17.82%) number of T's = 19,757,389 bp (33.11%) number of G's = 14,695,039 bp (24.62%) number of N's = 480 bp (0%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 304,341 number of insertions = 4,208 mapped reads with insertion percentage = 0.41% number of deletions = 11,416 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.0193X std coverageData = 0.1998X There is a 1.74% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6193275 0.024847581021673764 0.3457095360917107 chr2 243199373 5291701 0.021758695076898902 0.24410873173465075 chr3 198022430 4236558 0.021394333965096782 0.15931905794815146 chr4 191154276 2623010 0.013721953046972383 0.1547722487577898 chr5 180915260 3491888 0.019301235285514334 0.15063800332423657 chr6 171115067 3738626 0.021848607872736302 0.16656872331883182 chr7 159138663 3581927 0.022508213481723167 0.23807577847305497 chr8 146364022 5164831 0.035287572242309655 0.2622632887847026 chr9 141213431 2163731 0.015322416463346181 0.15633897926023754 chr10 135534747 2554517 0.018847690769659236 0.21455963366054906 chr11 135006516 2984927 0.022109503218348366 0.17770035388695107 chr12 133851895 1926901 0.014395769294114215 0.13376008310957083 chr13 115169878 1339240 0.01162838776298782 0.11758954962726055 chr14 107349540 1114654 0.0103834073252666 0.11513027416439857 chr15 102531392 1545680 0.01507518789952642 0.1340620238953382 chr16 90354753 1836518 0.020325637988297084 0.1607793065662816 chr17 81195210 1496267 0.018428020569193675 0.15254169984542898 chr18 78077248 1531583 0.019616252355615812 0.2466275033963629 chr19 59128983 1334332 0.022566462879972077 0.24389249796632176 chr20 63025520 1126153 0.017868206402739714 0.14809603968750432 chr21 48129895 498107 0.010349222660884675 0.1318858503248666 chr22 51304566 1181632 0.023031712226159365 0.16541177036375215 chrMT 16571 6265 0.3780701225031682 0.7476012816046229 chrX 155270560 2554667 0.01645300306767748 0.14928332618837611 chrY 59373566 179535 0.0030238203984581285 0.12185998100071097