BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975320.sorted.bam outfile = /mainsd/zhouyj/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 = 4,995,320 number of mapped reads = 4,940,674 (98.91%) number of supplementary alignments = 31,549 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,469,047 number of mapped paired reads (second in pair) = 2,471,627 number of mapped paired reads (both in pair) = 4,915,770 number of mapped paired reads (singletons) = 24,904 number of mapped bases = 456,529,011 bp number of sequenced bases = 456,237,181 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 390,880 duplication rate = 3.55% >>>>>>> Insert size mean insert size = 99,411.8479 std insert size = 2,960,749.8195 median insert size = 175 >>>>>>> Mapping quality mean mapping quality = 52.7575 >>>>>>> ACTG content number of A's = 135,736,286 bp (29.75%) number of C's = 86,960,081 bp (19.06%) number of T's = 137,907,362 bp (30.23%) number of G's = 95,621,277 bp (20.96%) number of N's = 12,175 bp (0%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,940,794 number of insertions = 76,109 mapped reads with insertion percentage = 1.5% number of deletions = 157,223 mapped reads with deletion percentage = 3.1% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.1475X std coverageData = 2.2573X There is a 9.58% of reference with a coverageData >= 1X There is a 2.86% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 34573287 0.13870893023773048 2.44506130529745 chr2 243199373 41527379 0.17075446571977798 1.9516324648910388 chr3 198022430 31246514 0.1577928015528342 0.6335811257511403 chr4 191154276 32866375 0.17193638399174496 1.9277489962099272 chr5 180915260 28294349 0.1563955909523608 0.5283666089639627 chr6 171115067 27178049 0.1588290819533735 1.5644115244117802 chr7 159138663 24342332 0.15296302948077425 2.089627055283439 chr8 146364022 23291307 0.1591327341359887 0.7700314006537444 chr9 141213431 19320206 0.1368156404329557 2.9610230618458084 chr10 135534747 26768354 0.1975017815911074 6.450816931867298 chr11 135006516 21299646 0.15776754064226056 2.2461366379023415 chr12 133851895 19546413 0.1460301551950385 0.5115541533636274 chr13 115169878 14538512 0.1262353685917771 0.45902938447423486 chr14 107349540 12966508 0.12078773695723335 0.5545800251466678 chr15 102531392 11918262 0.11624012673113811 0.4464504681943543 chr16 90354753 16046965 0.1775995668982682 3.7416428465847424 chr17 81195210 9541752 0.11751619338135834 1.7022820323726358 chr18 78077248 13064511 0.1673280159669562 2.9262727493789162 chr19 59128983 5333134 0.09019492183723167 1.4689064842530137 chr20 63025520 8555859 0.13575229526071345 0.6488677638178998 chr21 48129895 5801702 0.12054258585022884 0.8518088985684177 chr22 51304566 3462948 0.06749785194557537 0.3545412192294475 chrMT 16571 84236 5.083338362199022 5.814330015092973 chrX 155270560 14654583 0.09438095025869682 0.9596822782325517 chrY 59373566 10305828 0.17357603213524347 4.370767568935085