BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716623.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 = 624,001 number of mapped reads = 571,346 (91.56%) number of supplementary alignments = 2,503 (0.4%) number of secondary alignments = 0 number of mapped bases = 32,825,163 bp number of sequenced bases = 32,816,223 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,048 duplication rate = 1.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9532 >>>>>>> ACTG content number of A's = 8,040,011 bp (24.5%) number of C's = 6,305,643 bp (19.22%) number of T's = 10,371,715 bp (31.61%) number of G's = 8,098,086 bp (24.68%) number of N's = 768 bp (0%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 159,514 number of insertions = 2,020 mapped reads with insertion percentage = 0.35% number of deletions = 5,230 mapped reads with deletion percentage = 0.91% homopolymer indels = 41.17% >>>>>>> Coverage mean coverageData = 0.0106X std coverageData = 0.1204X There is a 1.01% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2693922 0.010808085408942672 0.16831618690551714 chr2 243199373 2801894 0.011520975426198982 0.12914755467458247 chr3 198022430 2177970 0.010998602532046495 0.10835987693817765 chr4 191154276 2085452 0.010909784722785903 0.11109522066988232 chr5 180915260 1949344 0.010774900912172914 0.10760937862138026 chr6 171115067 1879059 0.010981259762473166 0.11064752175457263 chr7 159138663 1729548 0.010868182297095207 0.12609840113137058 chr8 146364022 1664980 0.011375609779293985 0.1177595434861422 chr9 141213431 1389448 0.009839347363495473 0.11668071227682265 chr10 135534747 1548728 0.011426796701808135 0.12331970964455193 chr11 135006516 1537138 0.011385657859654714 0.1210255280593501 chr12 133851895 1506132 0.011252227695394227 0.10942378485785417 chr13 115169878 1029067 0.008935209604025107 0.09749341339100369 chr14 107349540 982072 0.009148357785231312 0.1020452638851322 chr15 102531392 927523 0.009046234347427956 0.0986399020047581 chr16 90354753 949665 0.010510404472025949 0.11067723963373761 chr17 81195210 893658 0.011006289656742066 0.11055268493594228 chr18 78077248 915051 0.011719816251720347 0.17539348655236262 chr19 59128983 669269 0.011318797754393983 0.1307104596810368 chr20 63025520 706980 0.011217360840497627 0.11096906790204195 chr21 48129895 427258 0.008877185375118729 0.10036022626239999 chr22 51304566 380226 0.007411153229519571 0.08878459594757182 chrMT 16571 1943 0.1172530324060105 0.3560877204697027 chrX 155270560 1880639 0.012112012734416621 0.11994000685646791 chrY 59373566 98197 0.0016538841544400415 0.05102098886744948