BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240240.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 672,741 number of mapped reads = 511,526 (76.04%) number of supplementary alignments = 2,449 (0.36%) number of secondary alignments = 0 number of mapped bases = 31,973,637 bp number of sequenced bases = 31,954,535 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,198 duplication rate = 6.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2942 >>>>>>> ACTG content number of A's = 8,282,167 bp (25.92%) number of C's = 5,484,846 bp (17.16%) number of T's = 10,548,143 bp (33.01%) number of G's = 7,622,349 bp (23.85%) number of N's = 17,030 bp (0.05%) GC percentage = 41.02% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 293,278 number of insertions = 2,239 mapped reads with insertion percentage = 0.43% number of deletions = 10,792 mapped reads with deletion percentage = 2.09% homopolymer indels = 49.7% >>>>>>> Coverage mean coverageData = 0.0103X std coverageData = 0.1451X There is a 0.82% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 2435662 0.009771939545137583 0.17360974775534566 chr2 243199373 3410680 0.014024213787755119 0.17902611064971205 chr3 198022430 2026355 0.010232956943311926 0.13071111875039756 chr4 191154276 1965440 0.010281956758320174 0.13147683927341405 chr5 180915260 1624654 0.008980193268384326 0.11885287047043248 chr6 171115067 1765483 0.010317519263221865 0.13814177996171104 chr7 159138663 1991802 0.012516141347750295 0.1980301199242323 chr8 146364022 1782967 0.012181730015590853 0.16133789608156332 chr9 141213431 1209927 0.008568073103471298 0.1319812468976252 chr10 135534747 1482999 0.01094183619201355 0.14234278537620249 chr11 135006516 1369420 0.0101433622655665 0.1387405065286564 chr12 133851895 1576650 0.011779063718149078 0.14309334806218 chr13 115169878 793929 0.00689354728673065 0.1048823170495572 chr14 107349540 1043147 0.009717293618584671 0.1274265177409464 chr15 102531392 879071 0.00857367663554202 0.12417003552117274 chr16 90354753 990292 0.010960043241997463 0.13729717007163086 chr17 81195210 855071 0.010531052262812054 0.13497314943659927 chr18 78077248 712136 0.009120915737194016 0.15434865514935558 chr19 59128983 596946 0.010095658164795428 0.14810364293363584 chr20 63025520 732297 0.011619055265232242 0.14125977240454307 chr21 48129895 525959 0.010927906657598152 0.13638069345294138 chr22 51304566 309526 0.006033108242256644 0.09921339727592922 chrMT 16571 13584 0.8197453382415062 1.2137052599342442 chrX 155270560 1797691 0.011577796847000487 0.13979266401625406 chrY 59373566 81949 0.0013802270188723379 0.045279584736192105