BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505923.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 9,229,522 number of mapped reads = 7,456,872 (80.79%) number of supplementary alignments = 258 (0%) number of secondary alignments = 0 number of mapped bases = 349,978,020 bp number of sequenced bases = 349,903,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 254,512 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5102 >>>>>>> ACTG content number of A's = 106,818,316 bp (30.53%) number of C's = 68,807,693 bp (19.66%) number of T's = 103,939,330 bp (29.71%) number of G's = 70,336,995 bp (20.1%) number of N's = 1,092 bp (0%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,609,479 number of insertions = 14,985 mapped reads with insertion percentage = 0.2% number of deletions = 53,611 mapped reads with deletion percentage = 0.72% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.1131X std coverageData = 1.0054X There is a 9.16% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 37305393 0.1496702108517515 2.272737430747122 chr2 243199373 23054341 0.09479605442897256 0.6625929377663619 chr3 198022430 23357095 0.11795176435315939 0.439528918589654 chr4 191154276 16058649 0.08400884006382363 0.344919262666049 chr5 180915260 21021235 0.11619381913941366 0.4135690467143725 chr6 171115067 25438392 0.14866249036971127 0.6854110257853633 chr7 159138663 24202155 0.15208218131127568 1.6606777916296414 chr8 146364022 22836665 0.1560264926308188 1.2956422444921167 chr9 141213431 9661861 0.06842026945723031 0.5591544265604167 chr10 135534747 11741558 0.08663134922884387 1.470681147655145 chr11 135006516 19020267 0.14088406666238243 0.8574364647188566 chr12 133851895 10422203 0.07786369404781307 0.3732737424226942 chr13 115169878 10766808 0.09348631940028625 0.34829916898791374 chr14 107349540 13231293 0.12325430551449033 0.45949818460692105 chr15 102531392 6366091 0.062089189230943045 0.2855344784938892 chr16 90354753 11051565 0.12231304533586629 0.621452015331973 chr17 81195210 5309984 0.06539774944852042 0.3850240960573781 chr18 78077248 8967159 0.11484983435891592 1.1439998444224586 chr19 59128983 7686200 0.12999039743335344 1.5587879205143638 chr20 63025520 8543689 0.13555919887689938 0.4373484318398127 chr21 48129895 5494101 0.11415152682132383 0.4452831435225865 chr22 51304566 2198184 0.042845777118551205 0.2775563883138398 chrMT 16571 7615 0.45953774666586206 0.7782829500758329 chrX 155270560 25263419 0.16270578917213926 0.5866003935228611 chrY 59373566 972098 0.016372572265576906 0.20205500647701258