BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926934.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 16,214,250 number of mapped reads = 15,574,953 (96.06%) number of supplementary alignments = 139,364 (0.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,794,941 number of mapped paired reads (second in pair) = 7,780,012 number of mapped paired reads (both in pair) = 15,426,646 number of mapped paired reads (singletons) = 148,307 number of mapped bases = 1,468,535,468 bp number of sequenced bases = 1,467,457,863 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 893,181 duplication rate = 4.33% >>>>>>> Insert size mean insert size = 85,143.9434 std insert size = 2,901,674.7168 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.1712 >>>>>>> ACTG content number of A's = 414,354,582 bp (28.24%) number of C's = 300,402,046 bp (20.47%) number of T's = 420,480,615 bp (28.65%) number of G's = 332,156,809 bp (22.63%) number of N's = 63,811 bp (0%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 13,682,389 number of insertions = 231,714 mapped reads with insertion percentage = 1.46% number of deletions = 752,713 mapped reads with deletion percentage = 4.71% homopolymer indels = 52.32% >>>>>>> Coverage mean coverageData = 0.4744X std coverageData = 2.3789X There is a 22.98% of reference with a coverageData >= 1X There is a 10.89% of reference with a coverageData >= 2X There is a 5.29% of reference with a coverageData >= 3X There is a 2.85% of reference with a coverageData >= 4X There is a 1.6% of reference with a coverageData >= 5X There is a 0.95% of reference with a coverageData >= 6X There is a 0.59% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% 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 137261772 0.5506978135071527 2.872175032620348 chr2 243199373 146324094 0.6016631218864203 3.887690162523028 chr3 198022430 112098033 0.5660875538190295 1.287330671688211 chr4 191154276 99568948 0.5208826612908204 2.238468962529266 chr5 180915260 98162190 0.5425865678771377 1.2336541474787939 chr6 171115067 97679180 0.570839153515336 2.8169493301290562 chr7 159138663 87536197 0.550062413179882 1.9238399995607118 chr8 146364022 83187776 0.5683621894457096 1.500853702017556 chr9 141213431 72269336 0.5117738127898047 2.9185133788065314 chr10 135534747 13799486 0.10181511608975077 4.7053506886574485 chr11 135006516 12136386 0.0898948166324061 0.9074698700625727 chr12 133851895 74696633 0.5580543555248134 1.329165476866212 chr13 115169878 5502212 0.047774748880084775 0.3834970733478714 chr14 107349540 49584545 0.4618980668198485 1.1788645301179583 chr15 102531392 48971679 0.47762619861827293 1.204732511022595 chr16 90354753 53944692 0.5970321450604817 3.0461236204668998 chr17 81195210 45982601 0.5663215970498753 1.7935459824325606 chr18 78077248 43657769 0.559161216850266 3.0077716382933977 chr19 59128983 8302322 0.14041036356062475 1.9030333854643613 chr20 63025520 40963538 0.6499516069046316 1.6263401905422514 chr21 48129895 20901450 0.4342716725228675 1.8493471602944576 chr22 51304566 21392908 0.4169786369501693 1.1907604596473964 chrMT 16571 91371 5.513909842495926 3.70191635403499 chrX 155270560 90693622 0.5841005661343657 1.407259626541078 chrY 59373566 3826728 0.06445171240009401 2.0686289278416794