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
A6 F1 I1 R1	67	31.4	1402038	96.1%	1347358	109.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,071,304	A→G	intergenic (+93/‑13)	yeeP → / → isrC	pseudogene, CP4‑44 prophage, 50S ribosome‑binding GTPase family,Phage or Prophage Related, putative histone/novel sRNA, CP4‑44, putative prophage remnant

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,071,304	0	A	G	100.0%	100.8 / NA	27	intergenic (+93/‑13)	yeeP/isrC	pseudogene, CP4‑44 prophage, 50S ribosome‑binding GTPase family,Phage or Prophage Related, putative histone/novel sRNA, CP4‑44, putative prophage remnant
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/14); total (13/14)

TGGTCTCTGTTGCCCGTGCGGTATGGAACTGGATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATAATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTC  >  NC_000913/2071168‑2071433

tggtCTCTGTTGCCCGTGCGGTATGGAACTGGATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCaatgat                                                                                                                                 >  2:56400/1‑139 (MQ=255)

            cccGTGCGGTATGGAACTGGATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGa                                                                                                                     >  2:692434/1‑139 (MQ=255)

              cGTGCGGTATGGAACTGGATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGGCTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATc                                                                                                                   <  2:219485/139‑1 (MQ=255)

              cGTGCGGTATGGAACTGGATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATc                                                                                                                   <  1:692434/139‑1 (MQ=255)

                 gCGGTATGGAACTGGATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAat                                                                                                                <  1:624255/139‑1 (MQ=255)

                              ggATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTatcg                                                                                                   <  1:56400/139‑1 (MQ=255)

                              ggATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTatcg                                                                                                   <  2:407003/139‑1 (MQ=255)

                               gATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATaa                                                                                                                          <  2:501522/115‑1 (MQ=255)

                               gATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACGGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATaa                                                                                                                          >  1:501522/1‑115 (MQ=255)

                                                gTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATaaaa                                                                                                                        >  1:186328/1‑100 (MQ=255)

                                                gTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATaaaa                                                                                                                        <  2:186328/100‑1 (MQ=255)

                                                 tCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATcgatcgat                                                                                <  1:617294/139‑1 (MQ=255)

                                                                          tGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATatcg                                                                                      <  2:552568/108‑1 (MQ=255)

                                                                          tGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATatcg                                                                                      >  1:552568/1‑108 (MQ=255)

                                                                            aGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAAc                                                     >  2:99393/1‑139 (MQ=255)

                                                                                  cTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATatcttctgaac                                                                               >  2:115209/1‑99 (MQ=255)

                                                                                  cTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATatcttctgaac                                                                               <  1:115209/107‑9 (MQ=255)

                                                                                  cTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTa                                                       <  2:396713/131‑1 (MQ=255)

                                                                                  cTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTa                                                       >  1:396713/1‑131 (MQ=255)

                                                                                            cACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTatcg                                                                                                   >  1:54556/1‑77 (MQ=255)

                                                                                            cACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTatcg                                                                                                   <  2:54556/77‑1 (MQ=255)

                                                                                               tGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACg                                        >  1:627488/1‑133 (MQ=255)

                                                                                               tGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACg                                        <  2:627488/133‑1 (MQ=255)

                                                                                                             tctctcTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACg                                        <  2:209393/119‑1 (MQ=255)

                                                                                                             tctctcTTGTCCGTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACg                                        >  1:209393/1‑119 (MQ=255)

                                                                                                                         gTGCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACca        >  1:432629/1‑139 (MQ=255)

                                                                                                                           gCAATAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACcaca      >  2:240150/1‑139 (MQ=255)

                                                                                                                               tAGCTCAATGATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTAAAGAAAGACATTCAGGGAACAACAGAACCACAATTc  >  1:58174/1‑139 (MQ=255)

                                                                                                                                     aatgatAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAg                               <  2:373607/104‑1 (MQ=255)

TGGTCTCTGTTGCCCGTGCGGTATGGAACTGGATTTTCTTCTGAACCTGTCGTGACTGATGCCCTCCCTGACTCTGAGTCTGCTCACAAAAGCACTGTTTTCGTTACTGTCTCTCTTGTCCGTGCAATAGCTCAATAATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTC  >  NC_000913/2071168‑2071433

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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