BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818811.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 = 1,269,773 number of mapped reads = 1,234,691 (97.24%) number of supplementary alignments = 10,146 (0.8%) number of secondary alignments = 0 number of mapped bases = 83,856,258 bp number of sequenced bases = 83,822,643 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 439,376 duplication rate = 31.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6568 >>>>>>> ACTG content number of A's = 23,137,167 bp (27.6%) number of C's = 17,534,885 bp (20.92%) number of T's = 24,487,526 bp (29.21%) number of G's = 18,658,080 bp (22.26%) number of N's = 4,985 bp (0.01%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 426,420 number of insertions = 10,588 mapped reads with insertion percentage = 0.85% number of deletions = 21,142 mapped reads with deletion percentage = 1.7% homopolymer indels = 40.4% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.3306X There is a 1.53% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 6736015 0.027025068073952763 0.48207152690159594 chr2 243199373 7397532 0.03041756197290854 0.4493520434177974 chr3 198022430 5708724 0.028828673600258314 0.2703206233284227 chr4 191154276 5540420 0.028984023355041244 0.2902988126377776 chr5 180915260 5171228 0.028583702668310014 0.2765663717084828 chr6 171115067 4994683 0.02918903102787553 0.2957601347986213 chr7 159138663 4578166 0.02876840808949111 0.31712665846740035 chr8 146364022 4355789 0.029759970657269857 0.3172701879416323 chr9 141213431 3586649 0.02539878094173634 0.2897305993811393 chr10 135534747 4093706 0.030204106995529344 0.35621031158551947 chr11 135006516 3984720 0.029515019852819548 0.30737149002498143 chr12 133851895 3898158 0.029122919776369247 0.28625892992064667 chr13 115169878 2763947 0.02399887060746908 0.2452365891056357 chr14 107349540 2620668 0.024412475358534372 0.26482890469729137 chr15 102531392 2468975 0.024080186095591094 0.2500210943048113 chr16 90354753 2417206 0.02675239453092191 0.33462656900006654 chr17 81195210 2260643 0.027842073442509725 0.2789607303679874 chr18 78077248 2266137 0.029024293991509537 0.39414811437280145 chr19 59128983 1628727 0.027545324092585866 0.402344510979029 chr20 63025520 1800940 0.028574774154977223 0.2802293631691557 chr21 48129895 1150585 0.02390582817602241 0.26167094138105673 chr22 51304566 988550 0.01926826551851155 0.23706653527803162 chrMT 16571 32269 1.947317603041458 2.6159738076578587 chrX 155270560 2629497 0.01693493602393139 0.22373499528861004 chrY 59373566 782324 0.013176301386377905 0.41450350226959587