BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16352032.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 1,289,884,690 number of mapped reads = 1,250,606,879 (96.95%) number of supplementary alignments = 29,094,813 (2.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 626,093,063 number of mapped paired reads (second in pair) = 624,513,816 number of mapped paired reads (both in pair) = 1,239,585,596 number of mapped paired reads (singletons) = 11,021,283 number of mapped bases = 112,987,841,751 bp number of sequenced bases = 112,915,723,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 421,953,553 duplication rate = 29.33% >>>>>>> Insert size mean insert size = 165,961.7533 std insert size = 3,950,413.7188 median insert size = 280 >>>>>>> Mapping quality mean mapping quality = 52.8137 >>>>>>> ACTG content number of A's = 33,137,002,635 bp (29.35%) number of C's = 23,164,592,030 bp (20.51%) number of T's = 32,811,177,004 bp (29.06%) number of G's = 23,800,597,167 bp (21.08%) number of N's = 2,355,053 bp (0%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 853,329,094 number of insertions = 14,644,840 mapped reads with insertion percentage = 1.15% number of deletions = 47,668,752 mapped reads with deletion percentage = 3.73% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 36.4984X std coverageData = 392.0862X There is a 91.8% of reference with a coverageData >= 1X There is a 91.72% of reference with a coverageData >= 2X There is a 91.68% of reference with a coverageData >= 3X There is a 91.64% of reference with a coverageData >= 4X There is a 91.61% of reference with a coverageData >= 5X There is a 91.58% of reference with a coverageData >= 6X There is a 91.54% of reference with a coverageData >= 7X There is a 91.51% of reference with a coverageData >= 8X There is a 91.46% of reference with a coverageData >= 9X There is a 91.41% of reference with a coverageData >= 10X There is a 91.36% of reference with a coverageData >= 11X There is a 91.28% of reference with a coverageData >= 12X There is a 91.19% of reference with a coverageData >= 13X There is a 91.08% of reference with a coverageData >= 14X There is a 90.93% of reference with a coverageData >= 15X There is a 90.75% of reference with a coverageData >= 16X There is a 90.51% of reference with a coverageData >= 17X There is a 90.2% of reference with a coverageData >= 18X There is a 89.8% of reference with a coverageData >= 19X There is a 89.29% of reference with a coverageData >= 20X There is a 88.64% of reference with a coverageData >= 21X There is a 87.83% of reference with a coverageData >= 22X There is a 86.83% of reference with a coverageData >= 23X There is a 85.61% of reference with a coverageData >= 24X There is a 84.15% of reference with a coverageData >= 25X There is a 82.43% of reference with a coverageData >= 26X There is a 80.43% of reference with a coverageData >= 27X There is a 78.14% of reference with a coverageData >= 28X There is a 75.56% of reference with a coverageData >= 29X There is a 72.71% of reference with a coverageData >= 30X There is a 69.6% of reference with a coverageData >= 31X There is a 66.25% of reference with a coverageData >= 32X There is a 62.71% of reference with a coverageData >= 33X There is a 59% of reference with a coverageData >= 34X There is a 55.18% of reference with a coverageData >= 35X There is a 51.29% of reference with a coverageData >= 36X There is a 47.38% of reference with a coverageData >= 37X There is a 43.5% of reference with a coverageData >= 38X There is a 39.7% of reference with a coverageData >= 39X There is a 36.01% of reference with a coverageData >= 40X There is a 32.47% of reference with a coverageData >= 41X There is a 29.11% of reference with a coverageData >= 42X There is a 25.96% of reference with a coverageData >= 43X There is a 23.02% of reference with a coverageData >= 44X There is a 20.31% of reference with a coverageData >= 45X There is a 17.84% of reference with a coverageData >= 46X There is a 15.6% of reference with a coverageData >= 47X There is a 13.58% of reference with a coverageData >= 48X There is a 11.78% of reference with a coverageData >= 49X There is a 10.19% of reference with a coverageData >= 50X There is a 8.78% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9031775292 36.23571831341596 889.172808302076 chr2 243199373 9688312313 39.83691320207475 367.03171681383776 chr3 198022430 7457842418 37.6616043849174 36.335297410053876 chr4 191154276 7609888502 39.810192380943654 269.49934304567665 chr5 180915260 6934578593 38.33053437836034 26.74272535138166 chr6 171115067 6048280415 35.346276169824364 98.86742385200768 chr7 159138663 6100097480 38.33196386725959 268.4982711624654 chr8 146364022 5710895858 39.018440324084565 577.6678493617468 chr9 141213431 4802929521 34.01184637316829 279.1060373581596 chr10 135534747 5979733197 44.119558484880635 878.5944942449078 chr11 135006516 5060130888 37.48064195657045 147.09261995611234 chr12 133851895 4958973229 37.04821085274885 38.830738803773976 chr13 115169878 3666900742 31.839060748158474 20.80793214320172 chr14 107349540 3368468063 31.3785048636445 35.62055138402276 chr15 102531392 3059325144 29.83793630735063 22.720805922163635 chr16 90354753 3601039775 39.85445873555761 358.15797504884824 chr17 81195210 2956038480 36.406562406821784 156.44718728837648 chr18 78077248 3124336596 40.01596721236896 482.2762467935198 chr19 59128983 2141309493 36.214211446863544 369.96021077707326 chr20 63025520 2252031177 35.73205230198815 48.55564025831093 chr21 48129895 1569624335 32.61225346533584 88.62327478737177 chr22 51304566 1259546130 24.550371013761232 31.271692467507016 chrMT 16571 294933823 17798.19099631887 3060.1608938941454 chrX 155270560 5921343349 38.135647536789975 74.05904266608582 chrY 59373566 389506938 6.560275291532935 262.92785987556056