BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708550.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,405,172 number of mapped reads = 3,616,408 (82.09%) number of supplementary alignments = 97 (0%) number of secondary alignments = 0 number of mapped bases = 180,343,470 bp number of sequenced bases = 180,326,832 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,497 duplication rate = 0.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5112 >>>>>>> ACTG content number of A's = 55,937,934 bp (31.02%) number of C's = 34,193,275 bp (18.96%) number of T's = 55,675,404 bp (30.87%) number of G's = 34,512,240 bp (19.14%) number of N's = 7,979 bp (0%) GC percentage = 38.1% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 285,640 number of insertions = 12,230 mapped reads with insertion percentage = 0.34% number of deletions = 9,717 mapped reads with deletion percentage = 0.27% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 0.0583X std coverageData = 0.2485X There is a 5.5% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 13796647 0.05535250802845542 0.2436346064995287 chr2 243199373 16164462 0.06646588681789077 0.2645406145695632 chr3 198022430 13590577 0.06863150300700785 0.2684976262247881 chr4 191154276 13877745 0.07259970998503847 0.2761675735568466 chr5 180915260 12381358 0.0684373335892174 0.26844270533648085 chr6 171115067 12179920 0.07117970505776677 0.27372628354794476 chr7 159138663 10072634 0.06329470042110383 0.258711547709131 chr8 146364022 9896359 0.06761469700525174 0.2666708092658646 chr9 141213431 7426331 0.052589409855780644 0.23647685644411837 chr10 135534747 7634232 0.05632675139755859 0.24334250359090556 chr11 135006516 8288195 0.06139107389453706 0.25525756437827957 chr12 133851895 8097381 0.060495079281470014 0.253717092513201 chr13 115169878 7129073 0.06190049971225983 0.255992811075751 chr14 107349540 5673952 0.05285492606675352 0.23700789772348932 chr15 102531392 4745692 0.0462852586649755 0.22215236422155085 chr16 90354753 3309383 0.03662655134478648 0.19642522896241255 chr17 81195210 2960574 0.036462421859614624 0.19620164737753246 chr18 78077248 5174047 0.06626830648539252 0.263569289052994 chr19 59128983 1323737 0.02238727833353738 0.15292292999308407 chr20 63025520 2819812 0.04474079706125392 0.21810383803427547 chr21 48129895 2119394 0.04403487686810869 0.2178263983360358 chr22 51304566 912203 0.01778015235525041 0.13664109344345313 chrMT 16571 100 0.006034638826866212 0.07744818888195831 chrX 155270560 10523304 0.06777398110755832 0.26765210979669934 chrY 59373566 246358 0.004149287580267623 0.06705907990333317