BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524953.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 = 1,549,806 number of mapped reads = 1,444,320 (93.19%) number of supplementary alignments = 3,441 (0.22%) number of secondary alignments = 0 number of mapped bases = 84,582,853 bp number of sequenced bases = 84,555,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,065 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8181 >>>>>>> ACTG content number of A's = 21,154,644 bp (25.02%) number of C's = 16,446,125 bp (19.45%) number of T's = 26,193,700 bp (30.98%) number of G's = 20,759,644 bp (24.55%) number of N's = 934 bp (0%) GC percentage = 44% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 407,959 number of insertions = 5,113 mapped reads with insertion percentage = 0.35% number of deletions = 16,212 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.89% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.2449X There is a 2.48% of reference with a coverageData >= 1X There is a 0.18% 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 9362626 0.037563099993239334 0.43471879622949144 chr2 243199373 7805377 0.03209456053984153 0.2816699758115836 chr3 198022430 4940522 0.024949304985298886 0.1720034313157348 chr4 191154276 5303165 0.027742853107821663 0.18911363058517 chr5 180915260 3438556 0.01900644533799968 0.15153518117005527 chr6 171115067 6083613 0.035552760529264205 0.27202720852929085 chr7 159138663 4513273 0.028360631633558463 0.2938729770533737 chr8 146364022 5848177 0.03995638354349131 0.27569089087270887 chr9 141213431 2483663 0.01758800832478888 0.18678137920843113 chr10 135534747 3379521 0.024934720245576584 0.2482457918438301 chr11 135006516 3526385 0.026120109639745093 0.22178303281505532 chr12 133851895 4530231 0.0338451017073759 0.19992481812311536 chr13 115169878 1799015 0.015620534042764202 0.1364654568659235 chr14 107349540 1973869 0.018387307481708817 0.15057583378750022 chr15 102531392 2417369 0.023576867073061877 0.1739004349841832 chr16 90354753 2518694 0.027875611590681897 0.1869978556374321 chr17 81195210 2483628 0.030588356135786827 0.26884289121631894 chr18 78077248 1682631 0.021550849230751574 0.28576698686118424 chr19 59128983 1955511 0.03307195390118582 0.28833111092078245 chr20 63025520 2138273 0.03392709810248293 0.19975072490806775 chr21 48129895 1293758 0.026880548981043903 0.1812444102060901 chr22 51304566 1113522 0.021704150075063496 0.1578233491813872 chrMT 16571 4792 0.28917989258342885 0.5792590117033689 chrX 155270560 3765644 0.024252144128288067 0.18983575773601988 chrY 59373566 221038 0.003722835175505544 0.08990800566473003