BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975211.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 2,569,912 number of mapped reads = 2,537,211 (98.73%) number of supplementary alignments = 100,843 (3.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,270,138 number of mapped paired reads (second in pair) = 1,267,073 number of mapped paired reads (both in pair) = 2,530,470 number of mapped paired reads (singletons) = 6,741 number of mapped bases = 342,336,178 bp number of sequenced bases = 342,167,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 620,133 duplication rate = 26.32% >>>>>>> Insert size mean insert size = 175,452.6975 std insert size = 4,121,990.7988 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.224 >>>>>>> ACTG content number of A's = 99,028,688 bp (28.94%) number of C's = 71,500,113 bp (20.9%) number of T's = 97,874,593 bp (28.6%) number of G's = 73,747,574 bp (21.55%) number of N's = 16,492 bp (0%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 3,130,166 number of insertions = 62,731 mapped reads with insertion percentage = 2.35% number of deletions = 65,747 mapped reads with deletion percentage = 2.49% homopolymer indels = 40.82% >>>>>>> Coverage mean coverageData = 0.1106X std coverageData = 2.3441X There is a 5.81% of reference with a coverageData >= 1X There is a 4.2% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 36137248 0.1449835826086066 6.576429794052345 chr2 243199373 23402979 0.09622960253273351 1.0994259393433217 chr3 198022430 24270587 0.12256483773075606 0.6000768113602568 chr4 191154276 18527935 0.09692660497952973 0.9630895433241672 chr5 180915260 28678310 0.15851791606744506 0.562057070017239 chr6 171115067 17323380 0.10123819195886473 0.5798490790664231 chr7 159138663 15695974 0.09863080224571197 0.8142065143507458 chr8 146364022 19486753 0.13313895541897586 1.2859464051164813 chr9 141213431 12693116 0.08988603923942617 1.7301272839343573 chr10 135534747 17303641 0.1276694086424937 5.117649536037771 chr11 135006516 13169545 0.09754747689363379 0.6759925797814579 chr12 133851895 13034407 0.09737932361734587 0.4386942208169321 chr13 115169878 6858239 0.05954889524151445 0.33881438484085585 chr14 107349540 10489789 0.09771619887705155 0.4427545667411512 chr15 102531392 8502916 0.08292987966066041 0.39839091916956504 chr16 90354753 9666296 0.10698159951806852 1.0413289756404578 chr17 81195210 8055191 0.09920771188349657 0.7657769896929114 chr18 78077248 7981638 0.10222745043472843 1.8364142389878888 chr19 59128983 8741022 0.14782973689907705 2.89647442664504 chr20 63025520 6148124 0.09754975444867413 0.5326273887080488 chr21 48129895 4118044 0.08556104267420488 0.679550039813944 chr22 51304566 4050594 0.07895192018581738 0.39041276565471167 chrMT 16571 266050 16.055156598877556 7.130363750388254 chrX 155270560 26507063 0.17071531782972896 0.7284290805049121 chrY 59373566 1227337 0.02067143819523995 1.1036876412464038