BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975306.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 = 3,972,704 number of mapped reads = 3,912,796 (98.49%) number of supplementary alignments = 16,334 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,955,360 number of mapped paired reads (second in pair) = 1,957,436 number of mapped paired reads (both in pair) = 3,899,116 number of mapped paired reads (singletons) = 13,680 number of mapped bases = 354,723,547 bp number of sequenced bases = 354,530,116 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 185,676 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 62,230.4209 std insert size = 2,394,843.9159 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 52.675 >>>>>>> ACTG content number of A's = 101,877,376 bp (28.74%) number of C's = 69,066,567 bp (19.48%) number of T's = 106,051,911 bp (29.91%) number of G's = 77,526,994 bp (21.87%) number of N's = 7,268 bp (0%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,629,743 number of insertions = 56,463 mapped reads with insertion percentage = 1.41% number of deletions = 109,371 mapped reads with deletion percentage = 2.74% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.1146X std coverageData = 1.0535X There is a 7.92% of reference with a coverageData >= 1X There is a 2.3% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.16% 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 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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% 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 33475519 0.1343046563563025 1.045613470297062 chr2 243199373 30303419 0.12460319542024477 1.3861266178568328 chr3 198022430 24046318 0.12143229431130605 0.4616250375182553 chr4 191154276 22543701 0.1179345891273706 0.8474413221279136 chr5 180915260 21753213 0.1202397907174884 0.4494929720528677 chr6 171115067 25614778 0.14969329381146781 0.8829574422247782 chr7 159138663 20580281 0.1293229477490332 1.1127875559977207 chr8 146364022 18150382 0.1240084943825881 0.568194342595541 chr9 141213431 15528966 0.10996805254310406 1.5587995406330208 chr10 135534747 16663006 0.12294268716198659 2.3889920996800686 chr11 135006516 13288765 0.09843054538197253 0.979934944977254 chr12 133851895 13884648 0.10373142643964808 0.4161872478254893 chr13 115169878 11970854 0.10394084119807785 0.4169695341918242 chr14 107349540 10645860 0.09917005699325773 0.4467561216292366 chr15 102531392 10467997 0.10209553187378945 0.4104001296832493 chr16 90354753 11877623 0.13145543101645135 1.646633030664339 chr17 81195210 7487203 0.09221237311905468 1.0150131532052413 chr18 78077248 10043730 0.12863837106553755 1.5934771351363648 chr19 59128983 5015746 0.0848271988713217 0.6554166618265342 chr20 63025520 7697720 0.12213655674717162 0.4884540975425745 chr21 48129895 4382445 0.09105453066124496 0.5331087508369053 chr22 51304566 3793953 0.07394961688205295 0.36923284813234813 chrMT 16571 95071 5.737191479089977 7.207577225318706 chrX 155270560 11242531 0.07240606976621969 0.48601453472727935 chrY 59373566 4169818 0.07023020985466832 1.5729956808728973