Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A12 F28 I1 R1	123	51.0	1731148	99.3%	1719029	138.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,728,350	T→C	S2P (TCC→CCC)	rnt →	RNase T

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,728,350	0	T	C	93.8%	97.0 / ‑2.0	32	S2P (TCC→CCC)	rnt	RNase T
Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (19/11); total (20/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

CCGGTCGCGGTCTGGGCAACTAATCTCCTGCCGGGCGTGAACTCATCGCGCCCGCATCTTTACTGCATCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGTCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGG  >  NC_000913/1728222‑1728485

ccGGTCGCGGTCTGGGCAACTAATCTCCTGCCGGGCGTGAACTCATCGCGCCCGCATCTTTACTGCATCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCt                                                                                                                              <  2:576382/140‑1 (MQ=255)

                             gCCGGGCGTGAACTCATCGCGCCCGCATCTTTACTGCATCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCg                                                                                                 <  2:648703/140‑1 (MQ=255)

                                      gAACTCATCGCGCCCGCATCTTTACTGCATCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCGCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTa                                                                                        <  2:431994/140‑1 (MQ=255)

                                            aTCGCGCCCGCATCTTTACTGCATCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGTCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCtgt                                                                                  >  1:315934/1‑140 (MQ=255)

                                                                 cATCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGAt                                                                            <  2:615780/125‑1 (MQ=255)

                                                                 cATCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGAt                                                                            >  1:615780/1‑125 (MQ=255)

                                                                 cATCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGc                                                             >  1:337331/1‑140 (MQ=255)

                                                                   tCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAg                                                              >  1:659407/1‑137 (MQ=255)

                                                                   tCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAg                                                              <  2:659407/137‑1 (MQ=255)

                                                                      aCAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGAt                                                        >  2:831747/1‑140 (MQ=255)

                                                                                 ttGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCaaa                                             >  1:808532/1‑140 (MQ=255)

                                                                                   gTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAc                                           >  2:574602/1‑140 (MQ=255)

                                                                                   gTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAc                                           >  2:54061/1‑140 (MQ=255)

                                                                                   gTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAc                                           >  2:620276/1‑140 (MQ=255)

                                                                                        aaTGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATg                                      <  1:831747/140‑1 (MQ=255)

                                                                                         aTGCGCGCTGAATTTTATCCTTATAAAGAAAATCAGATCCCCTATACCCCTCAACTTCCCGGTTTGTGCGCCCTTTTTCGTGTTTTTTATCCTGTTGTGATCGTTTTTAAACCAGCCGGATTTACCGCAAAACCCGATgc                                     <  2:808532/140‑1 (MQ=255)

                                                                                           gcgcgcTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATgcgc                                   <  1:458404/140‑1 (MQ=255)

                                                                                              cgcTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACTGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCgctgc                                >  1:793581/1‑140 (MQ=255)

                                                                                              cgcTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCgctgc                                >  2:298678/1‑140 (MQ=255)

                                                                                              cgcTGCAATTTATCCGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCgctgc                                >  2:466614/1‑140 (MQ=255)

                                                                                                           ccGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTgccgc                   >  2:713905/1‑140 (MQ=255)

                                                                                                           ccGTATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTgccgc                   >  1:469525/1‑140 (MQ=255)

                                                                                                              tATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCAt                >  2:359073/1‑140 (MQ=255)

                                                                                                              tATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCAt                <  1:620276/140‑1 (MQ=255)

                                                                                                              tATTAAGAGAATCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCAAAAACCGATGCGCTGCTTGAGATTGCCGCCAt                >  1:154788/1‑140 (MQ=255)

                                                                                                                       aaTCAGATGTCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGaa       <  2:315934/140‑1 (MQ=255)

                                                                                                                       aaTCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGaa       >  1:27882/1‑140 (MQ=255)

                                                                                                                        aTCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCa              >  2:359997/1‑132 (MQ=255)

                                                                                                                        aTCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCa              <  1:359997/132‑1 (MQ=255)

                                                                                                                        aTCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGaaa      >  1:589050/1‑140 (MQ=255)

                                                                                                                        aTCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCATTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGaaa      <  1:399235/140‑1 (MQ=255)

                                                                                                                         tCAGATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGaaaa     >  2:284545/1‑140 (MQ=255)

                                                                                                                            gATGCCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATgg  <  1:713905/140‑1 (MQ=255)

CCGGTCGCGGTCTGGGCAACTAATCTCCTGCCGGGCGTGAACTCATCGCGCCCGCATCTTTACTGCATCGACAAGTAATATTTGTCATAATGCGCGCTGCAATTTATCCGTATTAAGAGAATCAGATGTCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGG  >  NC_000913/1728222‑1728485

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A