BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524760.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 = 1,344,973 number of mapped reads = 1,239,625 (92.17%) number of supplementary alignments = 4,160 (0.31%) number of secondary alignments = 0 number of mapped bases = 71,743,214 bp number of sequenced bases = 71,720,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,728 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8147 >>>>>>> ACTG content number of A's = 17,299,820 bp (24.12%) number of C's = 14,733,969 bp (20.54%) number of T's = 21,722,143 bp (30.29%) number of G's = 17,956,352 bp (25.04%) number of N's = 8,703 bp (0.01%) GC percentage = 45.58% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 355,151 number of insertions = 5,206 mapped reads with insertion percentage = 0.42% number of deletions = 13,802 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2051X There is a 2.1% of reference with a coverageData >= 1X There is a 0.16% 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 5812193 0.023318670086683556 0.24226720141576535 chr2 243199373 5985427 0.024611194207314013 0.30997214691861386 chr3 198022430 4695663 0.0237127834457945 0.1680529968266015 chr4 191154276 4535792 0.023728435978068313 0.18748472223412235 chr5 180915260 4272434 0.02361566404072271 0.16589360783422044 chr6 171115067 4040273 0.02361143919605864 0.1764941923987242 chr7 159138663 3926489 0.0246733818544146 0.2475123643770691 chr8 146364022 3515625 0.024019734849866314 0.18825809661533258 chr9 141213431 3075667 0.021780272444481573 0.1867218422500372 chr10 135534747 3493935 0.025778887535017128 0.24432194809420857 chr11 135006516 3241536 0.024010218884546283 0.1922094516208295 chr12 133851895 3246793 0.024256608395420924 0.1707584641552018 chr13 115169878 2187916 0.01899729371945675 0.1495759118847841 chr14 107349540 2157333 0.020096341353675107 0.15671347693803514 chr15 102531392 2089841 0.02038245028410421 0.1568033311005618 chr16 90354753 2244486 0.024840818279919376 0.18640409944051978 chr17 81195210 2083358 0.025658631833084734 0.18171579187837233 chr18 78077248 1847432 0.023661592170871597 0.27096794483509457 chr19 59128983 1612106 0.027264226749849563 0.22733559053726826 chr20 63025520 1576932 0.0250205313657071 0.17848636484131147 chr21 48129895 956401 0.01987124634283952 0.16787567913028195 chr22 51304566 938727 0.018297143377063164 0.14775443061142562 chrMT 16571 24099 1.4542876108864884 1.5251584384474264 chrX 155270560 3951206 0.025447232237714605 0.18265552826417103 chrY 59373566 231550 0.0038998836620323597 0.10831219609048699