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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,940,160	Δ1 bp	coding (453/1428 nt)	hsrA ←	putative multidrug or homocysteine efflux system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,940,157	0	G	.	100.0%	155.6 / NA	37	coding (456/1428 nt)	hsrA	putative multidrug or homocysteine efflux system
Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (18/19); total (18/19)

TGCGTCGTGCGGTGGTGAAATTGGGCATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAACGGGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCTATC  >  NC_000913/3940030‑3940283

tGCGTCGTGCGGTGGTGAAATTGGGCATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAAtt                                                                                                                    <  2:332614/139‑1 (MQ=255)

         cGGTGGTGAAATTGGGCATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCccacc                                                                                                           <  1:1241/139‑1 (MQ=255)

              gtgAAATTGGGCATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGAcc                                                                                                      >  2:298991/1‑139 (MQ=255)

                         cATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGa                                                                                           <  1:317348/139‑1 (MQ=255)

                         cATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGa                                                                                           >  2:540510/1‑139 (MQ=255)

                                 tGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGc                                                                                                                 >  2:314477/1‑109 (MQ=255)

                                 tGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGc                                                                                                                 <  1:314477/109‑1 (MQ=255)

                                       cgTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACt                                                                             >  1:375148/1‑139 (MQ=255)

                                                 gCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGtt                                                                   <  2:133575/139‑1 (MQ=255)

                                                 gCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGtt                                                                   <  2:354279/139‑1 (MQ=255)

                                                    cGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCAt                                                                >  2:436294/1‑139 (MQ=255)

                                                             tATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGAt                                                       <  1:540510/139‑1 (MQ=255)

                                                               tGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATaa                                                     >  1:504252/1‑139 (MQ=255)

                                                                 gggATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGAC‑AAATTCAATACTGGAAGAAGTTCATTACGAGGATAAgcg                                                  >  2:496068/1‑139 (MQ=255)

                                                                     tatTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAgcgcgc                                               >  2:569899/1‑139 (MQ=255)

                                                                      atTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCa                                                                                  >  2:245058/1‑103 (MQ=255)

                                                                      atTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCa                                                                                  <  1:245058/103‑1 (MQ=255)

                                                                                    tCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGa                                >  2:275875/1‑139 (MQ=255)

                                                                                        gTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCaa                            <  2:375148/139‑1 (MQ=255)

                                                                                         tGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAAc                           >  1:258783/1‑139 (MQ=255)

                                                                                         tGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAAc                           >  2:262856/1‑139 (MQ=255)

                                                                                          gCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACa                          <  1:275875/139‑1 (MQ=255)

                                                                                          gCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACa                          <  1:23841/139‑1 (MQ=255)

                                                                                          gCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACa                          <  2:710655/139‑1 (MQ=255)

                                                                                                   cccAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGa                                                                                           >  2:190994/1‑65 (MQ=255)

                                                                                                   cccAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGa                                                                                           <  1:190994/65‑1 (MQ=255)

                                                                                                        gTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGTATCATCATTgc            >  2:520909/1‑139 (MQ=255)

                                                                                                        gTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTgc            >  2:683108/1‑139 (MQ=255)

                                                                                                          gACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTgcgc          <  2:512179/139‑1 (MQ=255)

                                                                                                           aCCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGcgcc         <  1:730458/139‑1 (MQ=255)

                                                                                                             cAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACa                                                                                         <  1:582179/57‑1 (MQ=255)

                                                                                                             cAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACa                                                                                         >  2:582179/1‑57 (MQ=255)

                                                                                                             cAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGcgccgc       >  2:288028/1‑139 (MQ=255)

                                                                                                              aGCACGCCGCCAAAAAC‑GGGCCTAAAATTGGCCCCACCGACCCCGGCAGGGCGA‑AAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCt     <  1:496068/139‑1 (MQ=255)

                                                                                                               gCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCt     <  1:32895/139‑1 (MQ=255)

                                                                                                               gCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCt     <  1:298991/139‑1 (MQ=255)

                                                                                                                  cgccgcCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCTATc  >  1:413700/1‑139 (MQ=255)

TGCGTCGTGCGGTGGTGAAATTGGGCATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAACGGGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCTATC  >  NC_000913/3940030‑3940283

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A