BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237805.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 = 2,702,219 number of mapped reads = 1,461,487 (54.08%) number of supplementary alignments = 9,057 (0.34%) number of secondary alignments = 0 number of mapped bases = 90,343,815 bp number of sequenced bases = 90,310,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,296 duplication rate = 5.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6977 >>>>>>> ACTG content number of A's = 24,505,572 bp (27.13%) number of C's = 17,861,074 bp (19.78%) number of T's = 27,210,391 bp (30.13%) number of G's = 20,656,383 bp (22.87%) number of N's = 77,348 bp (0.09%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 719,443 number of insertions = 7,004 mapped reads with insertion percentage = 0.48% number of deletions = 19,940 mapped reads with deletion percentage = 1.35% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 0.0292X std coverageData = 0.2996X There is a 2.1% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 7474326 0.029987191085072563 0.3969438084719381 chr2 243199373 7882230 0.032410568755865996 0.3953751306153253 chr3 198022430 6092421 0.030766317734814183 0.23807749026209263 chr4 191154276 5366878 0.02807615980298552 0.2559314759552783 chr5 180915260 5062657 0.02798358192669872 0.22362593072184758 chr6 171115067 5521778 0.032269385138364234 0.28198500157226963 chr7 159138663 4569576 0.028714430006239276 0.3001349541990831 chr8 146364022 4361411 0.02979838173618924 0.30522098623575633 chr9 141213431 4359860 0.030874258695690215 0.315770892657788 chr10 135534747 3945785 0.029112718969401995 0.3968591157843996 chr11 135006516 3768762 0.02791540817185446 0.26298617455630263 chr12 133851895 4527052 0.03382135157668108 0.251184021378467 chr13 115169878 2998318 0.026033873197295564 0.21649266886528298 chr14 107349540 2566936 0.023911942240274153 0.22613682297401436 chr15 102531392 2323737 0.02266366382697701 0.19856810409326564 chr16 90354753 2673650 0.029590585013275394 0.25779619567414847 chr17 81195210 2585733 0.031845881056283984 0.2509643151320082 chr18 78077248 3223229 0.04128256416004827 0.4885285195265214 chr19 59128983 1629409 0.02755685819930304 0.33641703795923933 chr20 63025520 1995322 0.031658953389039866 0.255987126493011 chr21 48129895 1169494 0.02429870250080537 0.23828795593537933 chr22 51304566 925490 0.018039135152220175 0.17919491910920818 chrMT 16571 35384 2.1352966024983404 2.0828761907634705 chrX 155270560 4960897 0.03195001679648737 0.2661437498768133 chrY 59373566 323480 0.005448215793540176 0.17695841402596557