BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525036.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 = 1,419,415 number of mapped reads = 1,305,404 (91.97%) number of supplementary alignments = 5,188 (0.37%) number of secondary alignments = 0 number of mapped bases = 76,291,352 bp number of sequenced bases = 76,265,643 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,375 duplication rate = 2.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.666 >>>>>>> ACTG content number of A's = 19,002,443 bp (24.92%) number of C's = 14,315,173 bp (18.77%) number of T's = 24,384,254 bp (31.97%) number of G's = 18,563,014 bp (24.34%) number of N's = 759 bp (0%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 377,790 number of insertions = 5,184 mapped reads with insertion percentage = 0.4% number of deletions = 15,321 mapped reads with deletion percentage = 1.16% homopolymer indels = 42.94% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.2297X There is a 2.25% of reference with a coverageData >= 1X There is a 0.15% 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 6139135 0.024630369927944935 0.39836919941960175 chr2 243199373 6404394 0.026333924800044612 0.25887579997140925 chr3 198022430 5057829 0.025541697473361984 0.1716181979624725 chr4 191154276 5006569 0.026191247743785756 0.19445963669133884 chr5 180915260 4592673 0.025385769005887064 0.17140089632436545 chr6 171115067 4357260 0.025463917797490035 0.20631373002003128 chr7 159138663 4127480 0.025936374745086303 0.26276555406954727 chr8 146364022 3899848 0.0266448540202045 0.24760302824106947 chr9 141213431 3167059 0.022427463008104376 0.19614524992177526 chr10 135534747 3697245 0.027278945671400413 0.24998315657401138 chr11 135006516 3467273 0.025682264106422832 0.21301893402262195 chr12 133851895 3427895 0.025609611279690886 0.17366784901959367 chr13 115169878 2398957 0.020829725980954845 0.15535054661983672 chr14 107349540 2330657 0.021710917438491118 0.16260831833338962 chr15 102531392 2231125 0.021760408753642983 0.16278701797494163 chr16 90354753 2236870 0.024756528303497217 0.1781192850658712 chr17 81195210 2128941 0.026220031945234208 0.19057398382490032 chr18 78077248 2026552 0.025955730406891392 0.317281566609242 chr19 59128983 1584582 0.026798735909257902 0.27956423128995994 chr20 63025520 1611027 0.025561502705570695 0.17404085227522598 chr21 48129895 1020677 0.02120671570133282 0.17595267946825235 chr22 51304566 921171 0.017954951611909162 0.1431006123729009 chrMT 16571 2628 0.15859030837004406 0.4080554413708574 chrX 155270560 4209226 0.02710897674356298 0.19014329801584023 chrY 59373566 244279 0.004114271997743912 0.13170462973296762