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
A1 F1 I2 R1	765	46.1	2269152	93.8%	2128464	105.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,187,588	G→A	pseudogene (162/2439 nt)	yqiG →	pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,187,588	0	G	A	100.0%	120.6 / NA	38	pseudogene (162/2439 nt)	yqiG	pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (20/18); total (20/18)

CCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGGTTGT  >  NC_000913/3187458‑3187723

ccGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGACAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCa                                                                                                                                 >  2:1050457/1‑139 (MQ=255)

     gAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTg                                                                                                                            <  1:253994/139‑1 (MQ=255)

      aaTTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGa                                                                                                                           <  2:234087/139‑1 (MQ=255)

       aTTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAc                                                                                                                          >  2:172484/1‑139 (MQ=255)

       aTTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGACAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAc                                                                                                                          <  1:1050457/139‑1 (MQ=255)

            acaaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCa                                                                                                                     <  1:450622/139‑1 (MQ=255)

             caaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                    <  2:442638/139‑1 (MQ=255)

              aaaGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                                   <  2:496172/139‑1 (MQ=255)

                     tAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTAtt                                                                                                            <  1:172484/139‑1 (MQ=255)

                       aTCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTaa                                                                                                          >  1:12430/1‑139 (MQ=255)

                                        tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                    <  2:589074/112‑1 (MQ=255)

                                        tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                    >  1:589074/1‑112 (MQ=255)

                                        tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCa                                                                                         >  2:309785/1‑139 (MQ=255)

                                               gTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCg                                                                                  <  2:12430/139‑1 (MQ=255)

                                                                                  aCCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCa                                                                                         >  2:970691/1‑97 (MQ=255)

                                                                                  aCCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCa                                                                                         <  1:970691/97‑1 (MQ=255)

                                                                                                      tAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGtttc                                                                                    >  2:671928/1‑81 (MQ=255)

                                                                                                      tAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTg                                                                                    <  1:671928/82‑1 (MQ=255)

                                                                                                        aGCACTCCGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGAtt                                                   <  1:918385/113‑1 (MQ=255)

                                                                                                        aGCACTCCGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGAtt                                                   >  2:918385/1‑113 (MQ=255)

                                                                                                           aCTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGc                      >  1:215745/1‑139 (MQ=255)

                                                                                                             tctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCaa                    >  1:470432/1‑139 (MQ=255)

                                                                                                                      taataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                                >  1:540487/1‑86 (MQ=255)

                                                                                                                      taataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                                <  2:540487/86‑1 (MQ=255)

                                                                                                                      taataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                                <  2:210711/86‑1 (MQ=255)

                                                                                                                      taataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                                >  1:210711/1‑86 (MQ=255)

                                                                                                                       aataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCg          >  1:191197/1‑139 (MQ=255)

                                                                                                                           agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATaa                                                                                                   >  2:154075/1‑46 (MQ=255)

                                                                                                                           agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATaa                                                                                                   <  1:154075/46‑1 (MQ=255)

                                                                                                                           agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCg                                                                                  <  2:1090252/63‑1 (MQ=255)

                                                                                                                           agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCg                                                                                  >  1:1090252/1‑63 (MQ=255)

                                                                                                                           agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGa                                                                               >  2:251592/1‑66 (MQ=255)

                                                                                                                           agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGa                                                                               >  1:2049/1‑66 (MQ=255)

                                                                                                                           agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGa                                                                               <  2:2049/66‑1 (MQ=255)

                                                                                                                           agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGa                                                                               <  1:251592/66‑1 (MQ=255)

                                                                                                                           agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATgg      >  2:200261/1‑139 (MQ=255)

                                                                                                                           agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATgg      >  2:883998/1‑139 (MQ=255)

                                                                                                                               gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGgttgt  >  1:582463/1‑139 (MQ=255)

CCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGGTTGT  >  NC_000913/3187458‑3187723

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A