BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716144.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 = 2,006,666 number of mapped reads = 1,776,113 (88.51%) number of supplementary alignments = 6,394 (0.32%) number of secondary alignments = 0 number of mapped bases = 101,181,652 bp number of sequenced bases = 101,152,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,964 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3086 >>>>>>> ACTG content number of A's = 25,363,970 bp (25.07%) number of C's = 19,449,840 bp (19.23%) number of T's = 32,134,840 bp (31.77%) number of G's = 24,203,080 bp (23.93%) number of N's = 881 bp (0%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 526,294 number of insertions = 8,421 mapped reads with insertion percentage = 0.47% number of deletions = 18,440 mapped reads with deletion percentage = 1.03% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.2694X There is a 2.91% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% 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 8093794 0.03247251287690874 0.33329381212763876 chr2 243199373 8440811 0.034707371552310705 0.432859262884813 chr3 198022430 6765927 0.0341674778963171 0.20821753520376138 chr4 191154276 6415160 0.03356011769258042 0.22488318176079197 chr5 180915260 5976242 0.03303337706283041 0.20065934056330825 chr6 171115067 5779269 0.03377416788201357 0.23232179359631522 chr7 159138663 5609320 0.035248002554853684 0.3447515831027514 chr8 146364022 5036740 0.03441241864752801 0.2525518321848598 chr9 141213431 4283964 0.030336802736561228 0.2324434109568724 chr10 135534747 4945418 0.03648819295025504 0.329559024658835 chr11 135006516 4469667 0.03310704647766779 0.25031108135835217 chr12 133851895 4640734 0.034670663422434175 0.2079084568164394 chr13 115169878 3144775 0.027305533830642766 0.18341011826753154 chr14 107349540 3058548 0.0284914867823374 0.19561991193807046 chr15 102531392 2957761 0.02884736998401426 0.1940802856518707 chr16 90354753 3063430 0.03390446986225506 0.22184858466310328 chr17 81195210 2908534 0.03582149735187581 0.21827738082818363 chr18 78077248 2613156 0.0334688538202576 0.35617864969382224 chr19 59128983 2261902 0.03825369362432633 0.31015946672998757 chr20 63025520 2173129 0.03448014391630565 0.21211728756127649 chr21 48129895 1314842 0.027318613514531874 0.2012305912041756 chr22 51304566 1248007 0.024325456724456063 0.17468936348805889 chrMT 16571 19735 1.190935972482047 1.426775812934799 chrX 155270560 5660613 0.036456447378047714 0.23280272279211447 chrY 59373566 300174 0.005055684208019441 0.14178832562640298