BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716762.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 = 1,348,702 number of mapped reads = 1,149,418 (85.22%) number of supplementary alignments = 3,072 (0.23%) number of secondary alignments = 0 number of mapped bases = 63,724,760 bp number of sequenced bases = 63,708,075 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,233 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.7582 >>>>>>> ACTG content number of A's = 14,860,717 bp (23.33%) number of C's = 13,462,262 bp (21.13%) number of T's = 19,013,829 bp (29.85%) number of G's = 16,369,663 bp (25.69%) number of N's = 1,604 bp (0%) GC percentage = 46.83% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 328,909 number of insertions = 3,916 mapped reads with insertion percentage = 0.34% number of deletions = 10,033 mapped reads with deletion percentage = 0.87% homopolymer indels = 35.43% >>>>>>> Coverage mean coverageData = 0.0206X std coverageData = 0.1802X There is a 1.87% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6269635 0.025153939335621555 0.22317436674259633 chr2 243199373 5425670 0.02230955587208689 0.21376802352298177 chr3 198022430 4329430 0.02186333134079811 0.1654840136233728 chr4 191154276 4057181 0.021224641608331065 0.18101312241383713 chr5 180915260 3879189 0.021442022082603755 0.15908450648192884 chr6 171115067 2678457 0.015652958251771015 0.1395140601556937 chr7 159138663 3677386 0.02310806142690793 0.2067616430034622 chr8 146364022 3906150 0.02668791104961573 0.1864191773995309 chr9 141213431 2793227 0.01978017940800546 0.16669727593597936 chr10 135534747 3328135 0.024555584996960225 0.24994423246647446 chr11 135006516 2689094 0.019918253427116065 0.18554185201618126 chr12 133851895 2996956 0.022390090181390408 0.16386035139964975 chr13 115169878 1125144 0.009769429468354565 0.10713277715500831 chr14 107349540 2051742 0.01911272279322296 0.15305979974187808 chr15 102531392 1277467 0.012459276862251125 0.12151936204120511 chr16 90354753 1733263 0.019182864680068353 0.1598793741729924 chr17 81195210 2602276 0.032049624602239465 0.205261371796814 chr18 78077248 1654852 0.02119506056361003 0.20238990151262642 chr19 59128983 1753244 0.029651178001826956 0.21477803752129374 chr20 63025520 1652208 0.026214904692575324 0.1816994202495556 chr21 48129895 882919 0.0183445029331562 0.1606465364345245 chr22 51304566 725510 0.014141236473962182 0.13165496331414134 chrMT 16571 24676 1.4891074769175066 1.8277904971484982 chrX 155270560 2010348 0.012947386806616785 0.1338418849977977 chrY 59373566 200601 0.0033786247570172893 0.10574279069203314