BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818827.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 749,371 number of mapped reads = 730,002 (97.42%) number of supplementary alignments = 6,303 (0.84%) number of secondary alignments = 0 number of mapped bases = 49,530,450 bp number of sequenced bases = 49,509,137 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 334,053 duplication rate = 38.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9096 >>>>>>> ACTG content number of A's = 14,382,977 bp (29.05%) number of C's = 10,345,186 bp (20.9%) number of T's = 13,802,113 bp (27.88%) number of G's = 10,975,800 bp (22.17%) number of N's = 3,061 bp (0.01%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 247,076 number of insertions = 5,718 mapped reads with insertion percentage = 0.77% number of deletions = 13,409 mapped reads with deletion percentage = 1.81% homopolymer indels = 39.73% >>>>>>> Coverage mean coverageData = 0.016X std coverageData = 0.2736X There is a 0.75% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 4048593 0.01624306083474111 0.30901059620839866 chr2 243199373 4376311 0.017994746228231436 0.4070960837228611 chr3 198022430 3427535 0.01730882203596835 0.24389493170642423 chr4 191154276 3313695 0.017335186370615114 0.25808595113080113 chr5 180915260 3083927 0.01704625137757865 0.24695875631304423 chr6 171115067 2936771 0.01716255062448709 0.25068575036955154 chr7 159138663 2734309 0.017181927687805194 0.2656345395188093 chr8 146364022 2565694 0.017529540148876203 0.25788815471425947 chr9 141213431 2096920 0.014849295744397004 0.23721942864595147 chr10 135534747 2332205 0.01720743242321469 0.28181525682985736 chr11 135006516 2309593 0.017107270585369375 0.26186421600189735 chr12 133851895 2298807 0.01717425816048402 0.2528769049139716 chr13 115169878 1583058 0.013745417009124556 0.2157707004628512 chr14 107349540 1507019 0.01403842997371018 0.23708194867493348 chr15 102531392 1463101 0.014269785784240596 0.22144897474186298 chr16 90354753 1419654 0.015712001337660677 0.29251340112035146 chr17 81195210 1300601 0.016018198610484535 0.2428021040753773 chr18 78077248 1288785 0.016506537218115066 0.26235841113277175 chr19 59128983 969791 0.016401279893483032 0.28539536598819976 chr20 63025520 1094939 0.017372946704763404 0.25673771535935036 chr21 48129895 665586 0.013828951839599899 0.2335727346119575 chr22 51304566 633571 0.012349212738686844 0.22716680768016348 chrMT 16571 60785 3.668155210910627 5.448573712933069 chrX 155270560 1537514 0.00990216046106873 0.18475673853324845 chrY 59373566 481686 0.008112802252773567 0.3952036343841844