BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618624.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 46,316,672 number of mapped reads = 42,433,788 (91.62%) number of supplementary alignments = 226,854 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,103,159 number of mapped paired reads (second in pair) = 20,330,629 number of mapped paired reads (both in pair) = 39,791,770 number of mapped paired reads (singletons) = 2,642,018 number of mapped bases = 3,963,572,713 bp number of sequenced bases = 3,960,692,568 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,408,085 duplication rate = 39.75% >>>>>>> Insert size mean insert size = 153,943.2337 std insert size = 3,899,872.4375 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.4989 >>>>>>> ACTG content number of A's = 1,116,058,425 bp (28.18%) number of C's = 828,311,791 bp (20.91%) number of T's = 1,145,454,394 bp (28.92%) number of G's = 868,657,192 bp (21.93%) number of N's = 2,210,766 bp (0.06%) GC percentage = 42.85% >>>>>>> Mismatches and indels general error rate = 0.0147 number of mismatches = 57,150,826 number of insertions = 777,569 mapped reads with insertion percentage = 1.8% number of deletions = 2,124,131 mapped reads with deletion percentage = 4.87% homopolymer indels = 52.5% >>>>>>> Coverage mean coverageData = 1.2804X std coverageData = 6.6342X There is a 20.19% of reference with a coverageData >= 1X There is a 14.35% of reference with a coverageData >= 2X There is a 11.14% of reference with a coverageData >= 3X There is a 9.1% of reference with a coverageData >= 4X There is a 7.6% of reference with a coverageData >= 5X There is a 6.48% of reference with a coverageData >= 6X There is a 5.58% of reference with a coverageData >= 7X There is a 4.86% of reference with a coverageData >= 8X There is a 4.26% of reference with a coverageData >= 9X There is a 3.76% of reference with a coverageData >= 10X There is a 3.34% of reference with a coverageData >= 11X There is a 2.98% of reference with a coverageData >= 12X There is a 2.67% of reference with a coverageData >= 13X There is a 2.4% of reference with a coverageData >= 14X There is a 2.16% of reference with a coverageData >= 15X There is a 1.95% of reference with a coverageData >= 16X There is a 1.77% of reference with a coverageData >= 17X There is a 1.61% of reference with a coverageData >= 18X There is a 1.46% of reference with a coverageData >= 19X There is a 1.33% of reference with a coverageData >= 20X There is a 1.22% of reference with a coverageData >= 21X There is a 1.12% of reference with a coverageData >= 22X There is a 1.02% of reference with a coverageData >= 23X There is a 0.94% of reference with a coverageData >= 24X There is a 0.87% of reference with a coverageData >= 25X There is a 0.8% of reference with a coverageData >= 26X There is a 0.73% of reference with a coverageData >= 27X There is a 0.68% of reference with a coverageData >= 28X There is a 0.63% of reference with a coverageData >= 29X There is a 0.58% of reference with a coverageData >= 30X There is a 0.53% of reference with a coverageData >= 31X There is a 0.49% of reference with a coverageData >= 32X There is a 0.46% of reference with a coverageData >= 33X There is a 0.42% of reference with a coverageData >= 34X There is a 0.39% of reference with a coverageData >= 35X There is a 0.36% of reference with a coverageData >= 36X There is a 0.34% of reference with a coverageData >= 37X There is a 0.31% of reference with a coverageData >= 38X There is a 0.29% of reference with a coverageData >= 39X There is a 0.27% of reference with a coverageData >= 40X There is a 0.25% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 338808026 1.3593066474245614 7.203477457704028 chr2 243199373 338045350 1.3899926871933177 7.5207027342436845 chr3 198022430 264570119 1.3360613694115357 5.887838075282388 chr4 191154276 225971277 1.182140843137613 6.008502383491329 chr5 180915260 237383007 1.3121226313357979 6.07782225041795 chr6 171115067 213444248 1.2473726115538382 5.570276765940044 chr7 159138663 199895749 1.2561105216775637 6.239270682369069 chr8 146364022 204473846 1.3970225961677931 6.986286913597184 chr9 141213431 166118684 1.176366035607477 6.863192123470271 chr10 135534747 200267054 1.4776067276681455 7.807691459317936 chr11 135006516 190335952 1.4098278930477697 6.932467234848277 chr12 133851895 175745808 1.3129870742584555 8.420033506810302 chr13 115169878 121100407 1.0514937508225892 4.980391868458062 chr14 107349540 125096992 1.165323968784589 5.538054262459295 chr15 102531392 132622093 1.2934779330802415 5.68634692581657 chr16 90354753 126733754 1.4026240988119352 10.736706953424603 chr17 81195210 104494291 1.2869514223807044 6.019277175708338 chr18 78077248 107051531 1.3710976467818128 6.607708194157027 chr19 59128983 62808089 1.0622217026800544 5.366835082811223 chr20 63025520 97614258 1.5488052776081815 5.894359930418762 chr21 48129895 48454768 1.0067499212287914 5.679065101058918 chr22 51304566 52509461 1.0234851416538637 6.20592723163491 chrMT 16571 46998 2.8361595558505823 17.099750734979555 chrX 155270560 223165460 1.4372683398578585 5.614585248698479 chrY 59373566 6815491 0.11478998920159184 3.876898201501761