BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524907.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 = 2,004,883 number of mapped reads = 1,857,808 (92.66%) number of supplementary alignments = 6,133 (0.31%) number of secondary alignments = 0 number of mapped bases = 107,854,452 bp number of sequenced bases = 107,819,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,263 duplication rate = 4.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7175 >>>>>>> ACTG content number of A's = 26,330,712 bp (24.42%) number of C's = 20,140,809 bp (18.68%) number of T's = 34,799,706 bp (32.28%) number of G's = 26,547,617 bp (24.62%) number of N's = 828 bp (0%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 545,823 number of insertions = 7,172 mapped reads with insertion percentage = 0.38% number of deletions = 21,058 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.15% >>>>>>> Coverage mean coverageData = 0.0348X std coverageData = 0.3088X There is a 3% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 11005976 0.04415626310515792 0.5582159075419707 chr2 243199373 9412584 0.03870315899210809 0.3805690649223128 chr3 198022430 7596020 0.038359391913330224 0.223144969279577 chr4 191154276 4817093 0.025200027437523816 0.22605847145027702 chr5 180915260 6504412 0.03595281017201092 0.21467158873237616 chr6 171115067 6818100 0.039845117788487906 0.2429727609630669 chr7 159138663 6352843 0.039920173264243144 0.3774633640241004 chr8 146364022 9298197 0.06352788665509615 0.3929022480309781 chr9 141213431 3994406 0.028286303729848472 0.2456832353342384 chr10 135534747 4585026 0.03382915526451678 0.34438256176045484 chr11 135006516 5418170 0.04013265552308601 0.2716188300399753 chr12 133851895 3609303 0.02696490027279778 0.19247350830107968 chr13 115169878 2265924 0.019674623602536072 0.15846060352779978 chr14 107349540 1983724 0.01847911039022617 0.161173686910134 chr15 102531392 2795996 0.027269658057504965 0.18868781984243987 chr16 90354753 3208611 0.035511258605288865 0.22862943978953562 chr17 81195210 2938101 0.03618564444873041 0.2243665308351975 chr18 78077248 2755958 0.03529783734180795 0.4113723917945643 chr19 59128983 2279994 0.038559668783750264 0.42544368054862985 chr20 63025520 2104921 0.033397915637982833 0.21359847551400651 chr21 48129895 928414 0.019289757436620213 0.20454311079247733 chr22 51304566 2108811 0.04110376842482207 0.23423255943046492 chrMT 16571 21814 1.3163961136925955 1.4214711193609777 chrX 155270560 4753080 0.030611598232143943 0.22033905857909117 chrY 59373566 296974 0.005001788169502907 0.16970424938835282