BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006055.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 4,503,138 number of mapped reads = 3,956,649 (87.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,009,726 number of mapped paired reads (second in pair) = 1,946,923 number of mapped paired reads (both in pair) = 3,647,238 number of mapped paired reads (singletons) = 309,411 number of mapped bases = 152,674,806 bp number of sequenced bases = 152,657,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 181,954 duplication rate = 4.22% >>>>>>> Insert size mean insert size = 67,721.9416 std insert size = 2,578,434.4519 median insert size = 91 >>>>>>> Mapping quality mean mapping quality = 45.8093 >>>>>>> ACTG content number of A's = 39,423,127 bp (25.82%) number of C's = 35,291,187 bp (23.12%) number of T's = 40,853,431 bp (26.76%) number of G's = 37,082,699 bp (24.29%) number of N's = 7,024 bp (0%) GC percentage = 47.41% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 703,390 number of insertions = 5,291 mapped reads with insertion percentage = 0.13% number of deletions = 13,495 mapped reads with deletion percentage = 0.34% homopolymer indels = 43.99% >>>>>>> Coverage mean coverageData = 0.0493X std coverageData = 0.3318X There is a 3.34% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 13200623 0.052961244176799864 0.3395881899834891 chr2 243199373 13324729 0.0547893229971444 0.37249031027989604 chr3 198022430 10505630 0.05305272741072817 0.31868518389000666 chr4 191154276 9139713 0.04781328041021693 0.31227414882912935 chr5 180915260 8425291 0.04657037222841235 0.2979393926717083 chr6 171115067 8740009 0.05107679383955125 0.3344454033343491 chr7 159138663 8482560 0.0533029487623633 0.3687294877973898 chr8 146364022 7446974 0.050879812526605755 0.336963093576715 chr9 141213431 6521924 0.04618487033290764 0.30555636739876096 chr10 135534747 7369211 0.0543713782857469 0.3362503574474363 chr11 135006516 7288602 0.05398703867004464 0.43837511833648646 chr12 133851895 7198933 0.05378282466602359 0.3227229839503944 chr13 115169878 4583370 0.03979660376127168 0.2815144707186094 chr14 107349540 4652199 0.04333692533754686 0.29453568904074234 chr15 102531392 4560321 0.04447731481105806 0.2949393105532869 chr16 90354753 5074452 0.05616142849729222 0.36633005191224355 chr17 81195210 4895312 0.06029065015042143 0.3561158974795478 chr18 78077248 3890556 0.04982957391121162 0.3295413161702551 chr19 59128983 3887392 0.06574427299045546 0.417312259433743 chr20 63025520 3521525 0.05587458857935643 0.3339198055742671 chr21 48129895 1987121 0.04128662653429849 0.3112397222099884 chr22 51304566 2371361 0.046221246662529025 0.3434499100456849 chrMT 16571 15120 0.9124373906221712 1.4768499327179028 chrX 155270560 4558108 0.02935590623232118 0.23666055449110165 chrY 59373566 1033770 0.01741128366788682 0.20440436772551804