BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630580.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 33,180,684 number of mapped reads = 32,552,814 (98.11%) number of supplementary alignments = 72,114 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,333,774 number of mapped paired reads (second in pair) = 16,219,040 number of mapped paired reads (both in pair) = 32,362,324 number of mapped paired reads (singletons) = 190,490 number of mapped bases = 3,170,562,771 bp number of sequenced bases = 3,168,288,247 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,206,441 duplication rate = 10.45% >>>>>>> Insert size mean insert size = 28,066.9492 std insert size = 1,637,423.8833 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.6157 >>>>>>> ACTG content number of A's = 930,736,861 bp (29.38%) number of C's = 630,027,063 bp (19.89%) number of T's = 938,783,846 bp (29.63%) number of G's = 668,256,650 bp (21.09%) number of N's = 483,827 bp (0.02%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 27,815,456 number of insertions = 583,602 mapped reads with insertion percentage = 1.76% number of deletions = 1,644,073 mapped reads with deletion percentage = 4.92% homopolymer indels = 54.09% >>>>>>> Coverage mean coverageData = 1.0242X std coverageData = 5.4148X There is a 16.63% of reference with a coverageData >= 1X There is a 11.78% of reference with a coverageData >= 2X There is a 8.97% of reference with a coverageData >= 3X There is a 7.22% of reference with a coverageData >= 4X There is a 5.98% of reference with a coverageData >= 5X There is a 5.05% of reference with a coverageData >= 6X There is a 4.34% of reference with a coverageData >= 7X There is a 3.77% of reference with a coverageData >= 8X There is a 3.3% of reference with a coverageData >= 9X There is a 2.91% of reference with a coverageData >= 10X There is a 2.59% of reference with a coverageData >= 11X There is a 2.31% of reference with a coverageData >= 12X There is a 2.07% of reference with a coverageData >= 13X There is a 1.87% of reference with a coverageData >= 14X There is a 1.69% of reference with a coverageData >= 15X There is a 1.53% of reference with a coverageData >= 16X There is a 1.39% of reference with a coverageData >= 17X There is a 1.27% of reference with a coverageData >= 18X There is a 1.16% of reference with a coverageData >= 19X There is a 1.06% of reference with a coverageData >= 20X There is a 0.98% of reference with a coverageData >= 21X There is a 0.9% of reference with a coverageData >= 22X There is a 0.83% of reference with a coverageData >= 23X There is a 0.76% of reference with a coverageData >= 24X There is a 0.7% of reference with a coverageData >= 25X There is a 0.65% of reference with a coverageData >= 26X There is a 0.6% of reference with a coverageData >= 27X There is a 0.56% of reference with a coverageData >= 28X There is a 0.52% of reference with a coverageData >= 29X There is a 0.48% of reference with a coverageData >= 30X There is a 0.45% of reference with a coverageData >= 31X There is a 0.42% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.36% of reference with a coverageData >= 34X There is a 0.34% of reference with a coverageData >= 35X There is a 0.32% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.28% of reference with a coverageData >= 38X There is a 0.26% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 272535334 1.0934188765772423 7.05017682531678 chr2 243199373 287855189 1.183618137864196 6.533472579313417 chr3 198022430 227865007 1.1507030137949523 4.577279460962147 chr4 191154276 208385403 1.0901425139974374 5.446455555648139 chr5 180915260 209288299 1.1568305459694224 4.611368681053502 chr6 171115067 199637041 1.1666830075226513 4.836735814968252 chr7 159138663 175387050 1.1021020705697395 4.715824508429929 chr8 146364022 165028091 1.1275181478683334 4.739991388953498 chr9 141213431 143316445 1.0148924502797472 6.861648813282128 chr10 135534747 153508831 1.1326160589653071 5.156529770215329 chr11 135006516 160369977 1.18786842110643 6.52141294686191 chr12 133851895 146125111 1.0916925083503675 4.502179631235939 chr13 115169878 101862691 0.8844560120138357 4.059518317413219 chr14 107349540 101880005 0.9490492926192324 4.2462663005139545 chr15 102531392 98037316 0.9561687799966668 4.261823152278539 chr16 90354753 98057776 1.0852531022911434 7.362993635861657 chr17 81195210 81089962 0.9987037658994908 4.794275422481507 chr18 78077248 88669996 1.135670099437931 7.6881934537656935 chr19 59128983 50822921 0.8595263848864101 5.075633076938421 chr20 63025520 75836490 1.2032663911380659 5.154200806941214 chr21 48129895 46124566 0.9583350638932414 5.705115588559013 chr22 51304566 37209217 0.7252613149480691 3.802940188959026 chrMT 16571 433 0.026129986120330698 0.18345113450240658 chrX 155270560 5565281 0.03584247393710695 1.6867908007249433 chrY 59373566 36104339 0.6080877641743803 5.135910373682156