BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004040.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 = 2,949,126 number of mapped reads = 2,681,910 (90.94%) number of supplementary alignments = 24,260 (0.82%) number of secondary alignments = 0 number of mapped bases = 178,778,715 bp number of sequenced bases = 178,692,591 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,410 duplication rate = 4.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3125 >>>>>>> ACTG content number of A's = 49,874,787 bp (27.91%) number of C's = 33,552,669 bp (18.78%) number of T's = 55,577,560 bp (31.1%) number of G's = 39,653,630 bp (22.19%) number of N's = 33,945 bp (0.02%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,403,991 number of insertions = 12,484 mapped reads with insertion percentage = 0.46% number of deletions = 49,721 mapped reads with deletion percentage = 1.83% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 0.0578X std coverageData = 0.5246X There is a 4.44% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.22% 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% 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 13108931 0.05259337347849577 0.7452027905830632 chr2 243199373 13841682 0.05691495758913819 0.5753453820897851 chr3 198022430 18277350 0.09229939254861179 0.37553574295784165 chr4 191154276 12074642 0.06316699920434947 0.3296748153871664 chr5 180915260 11141233 0.061582605027348164 0.3077090645863282 chr6 171115067 8660279 0.050610850066172136 0.30943781622406996 chr7 159138663 13476141 0.08468175329586626 1.1062212951701043 chr8 146364022 13704255 0.093631309202476 0.9077755112404781 chr9 141213431 6496188 0.046002621379548525 0.4600022276803137 chr10 135534747 10569743 0.07798548515385505 0.49724507191625367 chr11 135006516 5071217 0.0375627573412827 0.30509106509871986 chr12 133851895 5158627 0.038539812977619776 0.25844194371843887 chr13 115169878 9147207 0.07942360588417051 0.35099799237565166 chr14 107349540 3921060 0.036526099692648896 0.2785988838395185 chr15 102531392 5614501 0.05475884888015565 0.30179598181021394 chr16 90354753 5424117 0.06003134112933716 0.33653059302104277 chr17 81195210 2400126 0.029559945716009603 0.22303722726394942 chr18 78077248 4677587 0.05990973196186423 0.7946614704563882 chr19 59128983 1414706 0.02392576243024508 0.6458356429827212 chr20 63025520 3870027 0.06140412645544217 0.3302448468159448 chr21 48129895 1117982 0.023228432141811237 0.21976239253346103 chr22 51304566 1114856 0.021730151659405908 0.17758930845130183 chrMT 16571 8967 0.5411260636050932 0.8610860927116787 chrX 155270560 8105062 0.052199605643207574 0.3339283876598949 chrY 59373566 382229 0.006437696533167639 0.12655901038125786