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	1,684,175	T→C	S432P (TCT→CCT)	rstB →	sensory histidine kinase of RstAB two‑component system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,684,175	0	T	C	97.6%	153.0 / NA	41	S432P (TCT→CCT)	rstB	sensory histidine kinase of RstAB two‑component system
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (19/21); minor base A (1/0); total (20/21)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTAAAGTGGTTAATATTATGGCGCGTTACGATCTCGTAGACC  >  NC_000913/1684049‑1684283

gggctggCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACt                                                                                                  >  2:52762/1‑139 (MQ=255)

                       aGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTcacc                                                                           >  2:62676/1‑139 (MQ=255)

                              gCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACtg                                                                    <  1:145535/139‑1 (MQ=255)

                                   gggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGt                                                                               >  1:551133/1‑123 (MQ=255)

                                   gggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGt                                                                               <  2:551133/123‑1 (MQ=255)

                                   gggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCta                                                               <  1:62676/139‑1 (MQ=255)

                                      cGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCta                                                               >  2:617005/1‑136 (MQ=255)

                                      cGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCta                                                               <  1:617005/136‑1 (MQ=255)

                                        gTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCaa                                                                                 <  2:691892/116‑1 (MQ=255)

                                        gTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCaa                                                                                 <  2:396094/116‑1 (MQ=255)

                                        gTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCaa                                                                                 >  1:691892/1‑116 (MQ=255)

                                        gTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCaa                                                                                 >  1:396094/1‑116 (MQ=255)

                                             gTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGt                                                     <  2:448921/139‑1 (MQ=255)

                                              ttAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCaa                                                                                 <  1:355489/110‑1 (MQ=255)

                                              ttAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCaa                                                                                 >  2:355489/1‑110 (MQ=255)

                                                      gACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGa                                                                       <  1:385319/112‑1 (MQ=255)

                                                      gACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGa                                                                       >  2:385319/1‑112 (MQ=255)

                                                        cacCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACt                                          >  1:21603/1‑139 (MQ=255)

                                                            aGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTaaa                                       <  1:683918/138‑1 (MQ=255)

                                                            aGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTaaa                                       >  2:683918/1‑138 (MQ=255)

                                                             gCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGa                                                                       <  1:511150/105‑1 (MQ=255)

                                                             gCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGa                                                                       >  2:511150/1‑105 (MQ=255)

                                                                aaCTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTAAAGTGGt                                  <  2:21603/139‑1 (MQ=255)

                                                                     ggtggtGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAAt                                                         >  1:36917/1‑111 (MQ=255)

                                                                     ggtggtGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAAt                                                         <  2:36917/111‑1 (MQ=255)

                                                                          tgCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTAAAGTGGTTAATATTATg                        <  1:76804/139‑1 (MQ=255)

                                                                            cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTAAAGTGGTTAATATTATGgc                      >  1:326994/1‑139 (MQ=255)

                                                                               gCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTAAAGTGGTTAATATTATGGcgcg                   <  2:326994/139‑1 (MQ=255)

                                                                                 ttCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGc                                                                 >  2:357812/1‑91 (MQ=255)

                                                                                 ttCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGc                                                                 <  1:357812/91‑1 (MQ=255)

                                                                                    tcGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCaa                                                                                 <  2:148502/72‑1 (MQ=255)

                                                                                    tcGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCaa                                                                                 >  1:148502/1‑72 (MQ=255)

                                                                                           gCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCta                                                               <  2:235186/83‑1 (MQ=255)

                                                                                           gCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCta                                                               >  1:235186/1‑83 (MQ=255)

                                                                                           gCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATaa                                                            <  2:440665/86‑1 (MQ=255)

                                                                                           gCTGGCCGTTATGGCATAACATCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATaa                                                            >  1:440665/1‑86 (MQ=255)

                                                                                                ccgctctGGCATAACATCGCGCAGTTTACAACTGCCTGACACTACGCGCACGATGGTCAAGACACCACGACTGTACTATAAAACAAGTATGTTGTAATTAAGGTGGTTAATATTATGGCGCGTTACGAGCCGGTAGAcc  >  1:652375/7‑139 (MQ=255)

                                                                                                                tCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTaaa                                       <  1:532213/86‑1 (MQ=255)

                                                                                                                tCCCGCAATTTACCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTaaa                                       >  2:532213/1‑86 (MQ=255)

                                                                                                                           aCCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTAAAGTGGTTAATATTATGGCGCGTTACg              >  1:628345/1‑100 (MQ=255)

                                                                                                                           aCCCCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTAAAGTGGTTAATATTATGGCGCGTTACg              <  2:628345/100‑1 (MQ=255)

GGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTACGCGCACGATGGTCAAGTCACCACGACTGTGCTATAAAATAAGTATGTTGTAACTAAAGTGGTTAATATTATGGCGCGTTACGATCTCGTAGACC  >  NC_000913/1684049‑1684283

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