BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013344.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,331,140 number of mapped reads = 2,138,341 (91.73%) number of supplementary alignments = 21,453 (0.92%) number of secondary alignments = 0 number of mapped bases = 141,662,715 bp number of sequenced bases = 141,611,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,155 duplication rate = 1.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2103 >>>>>>> ACTG content number of A's = 39,320,541 bp (27.77%) number of C's = 27,725,429 bp (19.58%) number of T's = 42,201,462 bp (29.8%) number of G's = 32,328,688 bp (22.83%) number of N's = 35,767 bp (0.03%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,051,472 number of insertions = 10,276 mapped reads with insertion percentage = 0.48% number of deletions = 29,343 mapped reads with deletion percentage = 1.36% homopolymer indels = 44.95% >>>>>>> Coverage mean coverageData = 0.0458X std coverageData = 0.3578X There is a 4.09% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% 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 9574733 0.03841407881587585 0.4262753678230702 chr2 243199373 15257058 0.06273477522493448 0.4510471325656565 chr3 198022430 8629637 0.0435790884901271 0.22420874888496573 chr4 191154276 8388306 0.043882387438719916 0.23456878690084218 chr5 180915260 7055006 0.038996190813312265 0.21510899805603853 chr6 171115067 7094228 0.04145881554661694 0.2763086739093836 chr7 159138663 9562681 0.06009024343757369 0.7928864978583939 chr8 146364022 7987530 0.05457304254730032 0.3228855199380721 chr9 141213431 4533165 0.03210151447987975 0.30746820069445263 chr10 135534747 6737851 0.04971308944118957 0.3710125676859682 chr11 135006516 5982249 0.04431081682013037 0.3104509424868995 chr12 133851895 7452974 0.055680750728258274 0.25987625348899085 chr13 115169878 2903264 0.025208535863865376 0.17063436836594503 chr14 107349540 5085625 0.047374446131767306 0.2639000595718122 chr15 102531392 4205076 0.04101257105726215 0.22987606344348305 chr16 90354753 5393595 0.05969353930943733 0.2844928896107068 chr17 81195210 3534565 0.04353169355679972 0.2504002645424686 chr18 78077248 3259532 0.04174752675709062 0.5678001163599151 chr19 59128983 2852534 0.04824256828499824 0.387627194950201 chr20 63025520 3410532 0.05411350830584182 0.2598543996257266 chr21 48129895 2771684 0.057587576287045715 0.2819698139889176 chr22 51304566 1378346 0.026865951853096273 0.17558958356207313 chrMT 16571 228370 13.781304688914368 11.512897430920662 chrX 155270560 8069834 0.05197272425629173 0.2729396771502965 chrY 59373566 314340 0.005294275233527324 0.10003775586029981