BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618620.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 = 44,456,872 number of mapped reads = 40,661,702 (91.46%) number of supplementary alignments = 197,596 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,203,548 number of mapped paired reads (second in pair) = 19,458,154 number of mapped paired reads (both in pair) = 38,080,734 number of mapped paired reads (singletons) = 2,580,968 number of mapped bases = 3,780,949,259 bp number of sequenced bases = 3,778,280,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,944,226 duplication rate = 34.65% >>>>>>> Insert size mean insert size = 163,631.4032 std insert size = 4,038,615.3454 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 52.8409 >>>>>>> ACTG content number of A's = 1,057,943,807 bp (28%) number of C's = 793,356,534 bp (21%) number of T's = 1,082,945,364 bp (28.66%) number of G's = 841,962,593 bp (22.28%) number of N's = 2,072,059 bp (0.05%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 55,193,166 number of insertions = 728,075 mapped reads with insertion percentage = 1.76% number of deletions = 1,983,273 mapped reads with deletion percentage = 4.75% homopolymer indels = 52.48% >>>>>>> Coverage mean coverageData = 1.2214X std coverageData = 5.8749X There is a 21.61% of reference with a coverageData >= 1X There is a 15.16% of reference with a coverageData >= 2X There is a 11.65% of reference with a coverageData >= 3X There is a 9.36% of reference with a coverageData >= 4X There is a 7.69% of reference with a coverageData >= 5X There is a 6.44% of reference with a coverageData >= 6X There is a 5.45% of reference with a coverageData >= 7X There is a 4.67% of reference with a coverageData >= 8X There is a 4.03% of reference with a coverageData >= 9X There is a 3.5% of reference with a coverageData >= 10X There is a 3.05% of reference with a coverageData >= 11X There is a 2.68% of reference with a coverageData >= 12X There is a 2.36% of reference with a coverageData >= 13X There is a 2.09% of reference with a coverageData >= 14X There is a 1.85% of reference with a coverageData >= 15X There is a 1.65% of reference with a coverageData >= 16X There is a 1.47% of reference with a coverageData >= 17X There is a 1.31% of reference with a coverageData >= 18X There is a 1.18% of reference with a coverageData >= 19X There is a 1.06% of reference with a coverageData >= 20X There is a 0.95% of reference with a coverageData >= 21X There is a 0.86% of reference with a coverageData >= 22X There is a 0.78% of reference with a coverageData >= 23X There is a 0.71% of reference with a coverageData >= 24X There is a 0.64% of reference with a coverageData >= 25X There is a 0.58% of reference with a coverageData >= 26X There is a 0.53% of reference with a coverageData >= 27X There is a 0.49% of reference with a coverageData >= 28X There is a 0.44% of reference with a coverageData >= 29X There is a 0.41% of reference with a coverageData >= 30X There is a 0.37% of reference with a coverageData >= 31X There is a 0.34% of reference with a coverageData >= 32X There is a 0.32% of reference with a coverageData >= 33X There is a 0.29% of reference with a coverageData >= 34X There is a 0.27% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 342196484 1.3729012294015508 6.907821985705153 chr2 243199373 336988500 1.3856470756608406 6.198392811073229 chr3 198022430 269782282 1.3623824432414045 5.457735117440153 chr4 191154276 222872035 1.1659275411657546 5.459375523721439 chr5 180915260 237654393 1.3136227038006634 5.640894801840771 chr6 171115067 223491045 1.306086301564549 5.299770643285208 chr7 159138663 200872119 1.2622458629051068 5.70233147730584 chr8 146364022 201598243 1.3773756709145366 6.368645353250433 chr9 141213431 165474169 1.1718019159239887 6.199671684882341 chr10 135534747 193117421 1.4248554357798742 7.063340415660574 chr11 135006516 195198394 1.4458442435474743 6.247804744376389 chr12 133851895 179061851 1.3377610455197515 7.743695176937944 chr13 115169878 117454753 1.0198391718362332 4.541663879469418 chr14 107349540 117081276 1.0906546595355695 5.030015986714131 chr15 102531392 124317006 1.2124775015246063 5.093806619633232 chr16 90354753 125849358 1.3928360581097488 7.305130957503413 chr17 81195210 108360538 1.3345681106065248 5.665035741101737 chr18 78077248 103168731 1.321367410388235 5.879529335014219 chr19 59128983 63402857 1.0722805261169468 5.199645043349245 chr20 63025520 101199336 1.6056882354957167 5.6011203117618615 chr21 48129895 50415587 1.0474900682829247 5.651332445925669 chr22 51304566 54686232 1.0659135485134013 5.717980885412839 chrMT 16571 12799 0.7723734234506064 3.7282110661745334 chrX 155270560 10911071 0.07027134441970197 2.510164059213503 chrY 59373566 35782779 0.6026718860039499 3.922287377398383