BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716813.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 = 766,158 number of mapped reads = 693,669 (90.54%) number of supplementary alignments = 4,012 (0.52%) number of secondary alignments = 0 number of mapped bases = 40,065,376 bp number of sequenced bases = 40,054,269 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,274 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7545 >>>>>>> ACTG content number of A's = 10,371,964 bp (25.89%) number of C's = 8,059,192 bp (20.12%) number of T's = 12,268,713 bp (30.63%) number of G's = 9,354,151 bp (23.35%) number of N's = 249 bp (0%) GC percentage = 43.47% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 196,539 number of insertions = 2,833 mapped reads with insertion percentage = 0.41% number of deletions = 6,859 mapped reads with deletion percentage = 0.98% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.0129X std coverageData = 0.1438X There is a 1.21% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% 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 4684862 0.018795788677292802 0.20952141156143275 chr2 243199373 3790948 0.015587819792611061 0.18031831534735282 chr3 198022430 2205536 0.011137808984568062 0.11111637930150976 chr4 191154276 1719789 0.008996863873450573 0.10588773221355234 chr5 180915260 2931453 0.016203459011694205 0.13395816607483113 chr6 171115067 1535333 0.008972517890549054 0.10444067795017423 chr7 159138663 2559205 0.016081604254774968 0.20249359810023404 chr8 146364022 1834903 0.012536571316686009 0.1362337035091333 chr9 141213431 1113899 0.00788805280143643 0.11236498342070572 chr10 135534747 1938071 0.01429944012807284 0.13769719654932172 chr11 135006516 1722277 0.012756991669942805 0.1387782907586281 chr12 133851895 1664491 0.012435318902283752 0.11778772154097188 chr13 115169878 1185154 0.010290485850822904 0.10670326255073564 chr14 107349540 880145 0.008198870717098555 0.09795729651379842 chr15 102531392 1801096 0.017566288381220846 0.13984912226107707 chr16 90354753 1210723 0.013399660336628887 0.12469214194747781 chr17 81195210 1557233 0.019178877670246803 0.15097544089388437 chr18 78077248 1298375 0.01662936429316771 0.21726068416550323 chr19 59128983 633987 0.010722102221849477 0.15587971179018897 chr20 63025520 1122124 0.017804279917087554 0.1418688279058015 chr21 48129895 530041 0.011012718810211408 0.11205518736823984 chr22 51304566 489663 0.009544238226281847 0.10227666559873011 chrMT 16571 36774 2.219178082191781 2.012521531531862 chrX 155270560 1522151 0.009803217042561062 0.11056715924084728 chrY 59373566 97143 0.001636132146753658 0.05428679969854997