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
A3 F1 I2 R1	58	36.1	1832140	90.7%	1661750	105.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,649,905	G→A	P795S (CCG→TCG)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,649,905	0	G	A	100.0%	72.3 / NA	23	P795S (CCG→TCG)	yfhM	bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (13/10); total (13/10)

CGCCAGGACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATCCAGTTTCAGCGTGACACGGTCGGGTCGCA  >  NC_000913/2649788‑2650030

cGCCAGGACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCAt                                                                                                          >  2:531129/1‑139 (MQ=255)

          tACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAc                                                                                                             <  1:598770/126‑1 (MQ=255)

          tACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAc                                                                                                             >  2:598770/1‑126 (MQ=255)

                                  aTCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTc                                                                                                                >  2:822541/1‑99 (MQ=255)

                                  aTCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTc                                                                                                                <  1:822541/99‑1 (MQ=255)

                                  aTCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGata                                                                        >  2:45067/1‑139 (MQ=255)

                                       gACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCCCTGGACTCGACCATCGCATAACCTTTCCCCGCCGTTGGCGCGGCGATATGCaa                                                                   <  1:531129/139‑1 (MQ=255)

                                       gACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCaa                                                                   >  1:457628/1‑139 (MQ=255)

                                                 ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGAATCGACCATCGCATAACCTTTAcc                                                                                           >  2:384493/1‑105 (MQ=255)

                                                 ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACGGGACTCGACCATCGCATACCCTTTAcc                                                                                           <  1:384493/105‑1 (MQ=255)

                                                      tATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAcc                                                                                                            <  1:684708/83‑1 (MQ=255)

                                                      tATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAcc                                                                                                            >  2:684708/1‑83 (MQ=255)

                                                                              gCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCCCTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGTGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAAc                                         <  2:279291/126‑1 (MQ=255)

                                                                              gCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGTGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAAc                                         >  1:279291/1‑126 (MQ=255)

                                                                               cccTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAcc                                                                                                            >  1:723074/1‑58 (MQ=255)

                                                                               cccTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAcc                                                                                                            <  2:723074/58‑1 (MQ=255)

                                                                                           aaCATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAcc                                                                                                            >  2:848940/1‑46 (MQ=255)

                                                                                           aaCATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAcc                                                                                                            <  1:848940/46‑1 (MQ=255)

                                                                                                        tGCCACCACGGCGACCCTTCACTGGACTCGACCAGCGCATACCCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGGGTCGCCAGGGCGATAACTGGCTTTATCCAGTTTCAGCGTGACACGGTCGGGTCGCa  <  1:480221/139‑1 (MQ=255)

                                                                                                        tGCCACCACAGCGACCCTTCCCTGGACTCGACCATCGCa                                                                                                      <  1:505116/39‑1 (MQ=255)

                                                                                                        tGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCa                                                                                                      >  2:505116/1‑39 (MQ=255)

                                                                                                        tGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATCCAGTTTCAGCGTGACACGGTCGGGTCGCa  >  2:480221/1‑139 (MQ=255)

                                                                                                                caGCGACCTTTCACTGGACTCGACCATCGAATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATc                               <  1:104684/102‑1 (MQ=255)

                                                                                                                caGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATc                               >  2:104684/1‑102 (MQ=255)

CGCCAGGACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATCCAGTTTCAGCGTGACACGGTCGGGTCGCA  >  NC_000913/2649788‑2650030

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A