BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124822.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 29,890,158 number of mapped reads = 28,381,380 (94.95%) number of supplementary alignments = 92,361 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,524,865 number of mapped paired reads (second in pair) = 13,856,515 number of mapped paired reads (both in pair) = 27,579,718 number of mapped paired reads (singletons) = 801,662 number of mapped bases = 1,767,078,074 bp number of sequenced bases = 1,766,304,807 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,811,889 duplication rate = 12.97% >>>>>>> Insert size mean insert size = 98,569.4669 std insert size = 3,021,362.867 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 51.4813 >>>>>>> ACTG content number of A's = 492,698,668 bp (27.89%) number of C's = 314,931,782 bp (17.83%) number of T's = 534,253,561 bp (30.25%) number of G's = 424,420,761 bp (24.03%) number of N's = 35 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 14,600,951 number of insertions = 197,591 mapped reads with insertion percentage = 0.69% number of deletions = 524,501 mapped reads with deletion percentage = 1.83% homopolymer indels = 48.5% >>>>>>> Coverage mean coverageData = 0.5708X std coverageData = 4.7868X There is a 24.55% of reference with a coverageData >= 1X There is a 11.95% of reference with a coverageData >= 2X There is a 6.54% of reference with a coverageData >= 3X There is a 3.87% of reference with a coverageData >= 4X There is a 2.42% of reference with a coverageData >= 5X There is a 1.58% of reference with a coverageData >= 6X There is a 1.06% of reference with a coverageData >= 7X There is a 0.74% of reference with a coverageData >= 8X There is a 0.53% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 134220693 0.5384969251490852 4.7463465622101255 chr2 243199373 147015463 0.604505929380007 4.907627059844899 chr3 198022430 171649454 0.8668182387217448 2.0399322981242265 chr4 191154276 103747599 0.5427427582106508 2.1049246092105953 chr5 180915260 93040229 0.514275186073303 1.4093848005620189 chr6 171115067 87258132 0.5099383328996973 3.4048225264507033 chr7 159138663 117564794 0.7387569543675254 9.309437319146943 chr8 146364022 111924614 0.764700316857923 2.5331016032451172 chr9 141213431 69107339 0.4893821962303288 3.7372182060585306 chr10 135534747 85493032 0.6307831304691187 11.282787982290092 chr11 135006516 77418443 0.5734422700012495 3.2142541503312416 chr12 133851895 94894388 0.7089506502690903 1.7319209162716145 chr13 115169878 38188266 0.33158206523410577 1.0515232723583512 chr14 107349540 51098332 0.4759995431745679 1.8058992015809003 chr15 102531392 47428647 0.46257683695545654 1.5634027978342862 chr16 90354753 58851924 0.6513428684819713 11.483673185460122 chr17 81195210 38621004 0.4756561871075892 3.9144596594588292 chr18 78077248 45167435 0.5784967600292469 5.344745544889701 chr19 59128983 21379134 0.3615677611096406 4.251352095893725 chr20 63025520 51550743 0.8179344335437455 1.9781701382282337 chr21 48129895 20877156 0.4337669134744632 1.674029672781978 chr22 51304566 16073799 0.3133015295363769 1.1450048094094716 chrMT 16571 625244 37.73121718665138 22.1327007366952 chrX 155270560 67829732 0.4368486337654736 2.518756128437553 chrY 59373566 16052478 0.27036405392931934 4.064112768731608