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
A2 F1 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,210,944	G→A	pseudogene (1845/2001 nt)	yehQ →	pseudogene

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,210,944	0	G	A	100.0%	97.9 / NA	31	pseudogene (1845/2001 nt)	yehQ	pseudogene
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (16/15); total (16/15)

CGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAGTTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCGAA  >  NC_000913/2210811‑2211067

cGCTACCTTCTGCCAGCGTATTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATCCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCt                                                                                                                        <  1:661131/139‑1 (MQ=255)

               gCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCAc                                                                                                         >  2:390116/1‑139 (MQ=255)

                    ttGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCgg                                                                                                    <  2:626914/139‑1 (MQ=255)

                    ttGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCgg                                                                                                    <  2:170998/139‑1 (MQ=255)

                                                            gCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCgg                                                                                                    <  1:115502/99‑1 (MQ=255)

                                                            gCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCgg                                                                                                    >  2:115502/1‑99 (MQ=255)

                                                            gCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGAGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCg                                                            >  1:81310/1‑139 (MQ=255)

                                                                               aCTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCa                                         >  2:748140/1‑139 (MQ=255)

                                                                                cTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCa                                         >  2:597177/1‑138 (MQ=255)

                                                                                cTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCa                                         <  1:597177/138‑1 (MQ=255)

                                                                                 tGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTG‑TGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGc                                                                                     >  2:941077/1‑92 (MQ=255)

                                                                                 tGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTG‑TGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGc                                                                                     <  1:941077/92‑1 (MQ=255)

                                                                                      cATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGcac                                                                               <  2:263793/94‑1 (MQ=255)

                                                                                      cATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGcac                                                                               >  1:263793/1‑94 (MQ=255)

                                                                                                  cgcTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCgg                                                                                      <  1:775180/75‑1 (MQ=255)

                                                                                                  cgcTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCgg                                                                                      >  2:775180/1‑75 (MQ=255)

                                                                                                     tATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGGGAATGACCTCACCGCGGGGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACg                   <  1:748140/139‑1 (MQ=255)

                                                                                                                 agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACaa                                                                 <  2:379640/81‑1 (MQ=255)

                                                                                                                 agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACaa                                                                 >  1:379640/1‑81 (MQ=255)

                                                                                                                 agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTtttgcttt       >  1:833916/1‑139 (MQ=255)

                                                                                                                 agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTtttgcttt       >  1:618641/1‑139 (MQ=255)

                                                                                                                 agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTtttgcttt       >  2:20919/1‑139 (MQ=255)

                                                                                                                 agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTtttgcttt       >  2:346643/1‑139 (MQ=255)

                                                                                                                   tGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTtttgctttgc     >  2:603788/1‑139 (MQ=255)

                                                                                                                    gCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCg    <  1:886333/139‑1 (MQ=255)

                                                                                                                    gCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCg    <  2:618641/139‑1 (MQ=255)

                                                                                                                      tATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCGaa  <  1:346643/139‑1 (MQ=255)

                                                                                                                                gCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGc                                                                                     >  2:257540/1‑46 (MQ=255)

                                                                                                                                gCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGc                                                                                     <  1:257540/46‑1 (MQ=255)

                                                                                                                                gCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGcaca                                                                              >  2:578532/1‑53 (MQ=255)

                                                                                                                                gCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGcaca                                                                              <  1:578532/53‑1 (MQ=255)

CGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAGTTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCGAA  >  NC_000913/2210811‑2211067

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A