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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,630,986	A→G	intergenic (‑73/+16)	ydfI ← / ← ydfJ	putative NAD‑dependent D‑mannonate oxidoreductase/pseudogene, MFS transporter family, interrupted by Qin prophage,Phage or Prophage Related, putative transport protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,630,986	0	A	G	100.0%	128.7 / NA	36	intergenic (‑73/+16)	ydfI/ydfJ	putative NAD‑dependent D‑mannonate oxidoreductase/pseudogene, MFS transporter family, interrupted by Qin prophage,Phage or Prophage Related, putative transport protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (19/17); total (19/17)

ATAAACAGGGAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGAGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCATTTTCAGCGCAGAGATTAAACC  >  NC_000913/1630869‑1631121

aTAAACAGGGAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAg                                                                                                                    >  2:570233/1‑139 (MQ=255)

aTAAACAGGGAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAg                                                                                                                    <  1:323659/139‑1 (MQ=255)

       gggAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGaa                                                                                                                                      >  2:397941/1‑114 (MQ=255)

       gggAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGaa                                                                                                                                      <  1:397941/114‑1 (MQ=255)

        ggAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTgg                                                                                                            >  2:476720/1‑139 (MQ=255)

             gtCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGt                                                                                                       >  1:104694/1‑139 (MQ=255)

                 cTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTgcg                                                                                                   <  2:104694/139‑1 (MQ=255)

                 cTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTgcg                                                                                                   <  2:778573/139‑1 (MQ=255)

                  ttttGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGaa                                                                                                                                      >  2:393368/1‑103 (MQ=255)

                  ttttGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGaa                                                                                                                                      <  1:393368/103‑1 (MQ=255)

                                                  ttCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAg                                                                  >  1:291648/1‑139 (MQ=255)

                                                        taatataaatatGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACa                                                                                                                     >  2:581433/2‑82 (MQ=255)

                                                        aaatataaatatGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGATGGGATTAAGGGTTTACa                                                                                                                     <  1:581433/82‑1 (MQ=255)

                                                            ataaatatGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAg                                                        <  2:805226/139‑1 (MQ=255)

                                                              aaatatGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAgcg                                                      >  1:422835/1‑139 (MQ=255)

                                                               aatatGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAgcgc                                                     >  2:697450/1‑139 (MQ=255)

                                                                    ggCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTacaaca                                                                                     >  2:125679/1‑102 (MQ=255)

                                                                    ggCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTacaaca                                                                                     <  1:125679/102‑1 (MQ=255)

                                                                     gCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTaa                                               >  1:422670/1‑139 (MQ=255)

                                                                          cTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCAc                                          >  1:107082/1‑139 (MQ=255)

                                                                          cTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCAc                                          <  1:355096/139‑1 (MQ=255)

                                                                          cTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCAc                                          >  2:816754/1‑139 (MQ=255)

                                                                           tataTGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACg                                         <  2:291648/139‑1 (MQ=255)

                                                                                    tGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGct                                                                                              >  2:93477/1‑77 (MQ=255)

                                                                                    tGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGct                                                                                              <  1:93477/77‑1 (MQ=255)

                                                                                    tGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCAc                                <  1:816754/139‑1 (MQ=255)

                                                                                           tGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGc                         >  1:875996/1‑139 (MQ=255)

                                                                                              aTAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTacaaca                                                                                     >  2:683206/1‑76 (MQ=255)

                                                                                              aTAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTacaaca                                                                                     <  1:683206/76‑1 (MQ=255)

                                                                                               tAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGa                                                                                                                   <  2:132780/45‑1 (MQ=255)

                                                                                               tAAAAATCCCCTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGa                                                                                                                   >  1:132780/1‑45 (MQ=255)

                                                                                                       cccTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCa                                                                   <  2:225744/85‑1 (MQ=255)

                                                                                                       cccTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCa                                                                   >  1:225744/1‑85 (MQ=255)

                                                                                                       cccTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCATTTTCAGCGCa             <  1:697450/139‑1 (MQ=255)

                                                                                                        ccTCTCCGGTAAGGGAAGGGATTAAGGGTTTAGAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCg                                                                <  1:481926/87‑1 (MQ=255)

                                                                                                        ccTCTCCGGTAAGGGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCg                                                                >  2:481926/1‑87 (MQ=255)

                                                                                                                  aagggaagggATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCATTTTCAGCGCAGAGATTAAAcc  <  2:686946/139‑1 (MQ=255)

ATAAACAGGGAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGAGAAGGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCATTTTCAGCGCAGAGATTAAACC  >  NC_000913/1630869‑1631121

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A