BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006143.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 16,574,310 number of mapped reads = 14,578,270 (87.96%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,403,355 number of mapped paired reads (second in pair) = 7,174,915 number of mapped paired reads (both in pair) = 13,328,216 number of mapped paired reads (singletons) = 1,250,054 number of mapped bases = 563,127,694 bp number of sequenced bases = 563,064,631 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,145,266 duplication rate = 6.95% >>>>>>> Insert size mean insert size = 60,998.4231 std insert size = 2,408,374.894 median insert size = 110 >>>>>>> Mapping quality mean mapping quality = 47.4155 >>>>>>> ACTG content number of A's = 154,223,599 bp (27.39%) number of C's = 121,628,273 bp (21.6%) number of T's = 159,059,870 bp (28.25%) number of G's = 128,130,546 bp (22.76%) number of N's = 22,343 bp (0%) GC percentage = 44.36% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 2,629,209 number of insertions = 18,075 mapped reads with insertion percentage = 0.12% number of deletions = 49,669 mapped reads with deletion percentage = 0.34% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.1819X std coverageData = 0.883X There is a 9.53% of reference with a coverageData >= 1X There is a 4.39% of reference with a coverageData >= 2X There is a 2.04% of reference with a coverageData >= 3X There is a 0.99% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 47940912 0.19234019079936415 0.9599026520415733 chr2 243199373 49218118 0.20237765168909377 0.9926951693793715 chr3 198022430 38886966 0.19637657208832354 0.7332745356477807 chr4 191154276 34515829 0.18056529899441015 0.7487867961618027 chr5 180915260 35209778 0.19462027691859715 0.731980101561824 chr6 171115067 33006169 0.19288873609242135 0.8413469102820552 chr7 159138663 30553369 0.19199211821956805 1.2900579352138546 chr8 146364022 28893917 0.1974113351435505 0.9663600583543016 chr9 141213431 23769239 0.16832137588952145 0.8104318709201536 chr10 135534747 26837507 0.19801200499529467 0.7858145610079023 chr11 135006516 26687476 0.1976754662715687 1.3487911353772772 chr12 133851895 25690179 0.1919298863867411 0.7296864462550489 chr13 115169878 17881728 0.155263931077534 0.6604736273524497 chr14 107349540 17417156 0.16224714144094143 0.6961958017704437 chr15 102531392 17287156 0.16860354339088657 0.6972904654243893 chr16 90354753 17195502 0.19031098452562867 0.8589493769664843 chr17 81195210 16603738 0.20449159500911446 0.8782596019112981 chr18 78077248 14985713 0.19193444164425466 1.1936851316675865 chr19 59128983 12129723 0.20514005796446727 0.9893583830980386 chr20 63025520 12559048 0.19926924839334922 0.7583715859717619 chr21 48129895 7558964 0.1570534072430451 0.7658539208109888 chr22 51304566 7443259 0.14507985507566715 0.7135433933094123 chrMT 16571 44436 2.68155210910627 3.751209270526984 chrX 155270560 17265352 0.11119527101596079 0.6150215410342796 chrY 59373566 3546460 0.059731295236671485 0.504141990818792