BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716424.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 = 836,720 number of mapped reads = 769,306 (91.94%) number of supplementary alignments = 2,622 (0.31%) number of secondary alignments = 0 number of mapped bases = 44,701,923 bp number of sequenced bases = 44,688,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,809 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8528 >>>>>>> ACTG content number of A's = 10,687,264 bp (23.92%) number of C's = 8,215,878 bp (18.38%) number of T's = 14,593,570 bp (32.66%) number of G's = 11,190,649 bp (25.04%) number of N's = 857 bp (0%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 227,973 number of insertions = 2,588 mapped reads with insertion percentage = 0.34% number of deletions = 8,567 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.0144X std coverageData = 0.1712X There is a 1.36% of reference with a coverageData >= 1X There is a 0.05% 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 3743114 0.015017471109931558 0.2837151014235555 chr2 243199373 3568528 0.014673261513712866 0.20785410965663959 chr3 198022430 2625286 0.01325751835284518 0.12060477173920316 chr4 191154276 2878081 0.015056325499095819 0.1352925833222275 chr5 180915260 2616070 0.014460195342283454 0.1253892897297125 chr6 171115067 2454407 0.014343605405595289 0.14272298966449642 chr7 159138663 2570460 0.016152328739873854 0.23170164677414182 chr8 146364022 2403933 0.016424343681946646 0.19826147973015518 chr9 141213431 1485865 0.010522122361009698 0.1278978078443107 chr10 135534747 1966959 0.014512581043147555 0.17614545197004455 chr11 135006516 1592593 0.011796415811515349 0.13858111967419268 chr12 133851895 2251746 0.016822668069062453 0.13599143969595326 chr13 115169878 1417881 0.01231121387486405 0.11591227614249303 chr14 107349540 1487283 0.013854581957221243 0.12516007720194156 chr15 102531392 1603307 0.015637230400617208 0.131777968291216 chr16 90354753 1431221 0.01584001895284911 0.13784858664266045 chr17 81195210 1811961 0.022316107070848145 0.15952831803534895 chr18 78077248 855657 0.010959108087416196 0.20864990117938717 chr19 59128983 1021792 0.017280730162397687 0.22591361448990538 chr20 63025520 1356654 0.021525470952084173 0.15443215839717614 chr21 48129895 565098 0.011741101866106295 0.12075111224178019 chr22 51304566 371668 0.00724434546430039 0.08815605877578607 chrMT 16571 22870 1.3801218997043028 1.4754011161828182 chrX 155270560 2454058 0.015805043789369987 0.13827191105896672 chrY 59373566 145431 0.002449423367968163 0.10440276074946904