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	4,567,574	T→C	T316A (ACC→GCC)	mdtM ←	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,567,574	0	T	C	97.0%	115.9 / ‑4.1	33	T316A (ACC→GCC)	mdtM	multidrug efflux system protein
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (18/14); total (19/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.95e-01

CACCATCAGGATCACCATATTTAGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGTGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACCGCGGTTCGGTCGGATCTTTAACAAAACGCGCCACG  >  NC_000913/4567452‑4567710

cACCATCAGGATCACCATATTTAGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACcac                                                                                                                          <  1:396415/139‑1 (MQ=255)

     tCAGGATCACCATATTTAGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCa                                                                                                                     >  1:673031/1‑139 (MQ=255)

             aCCATATTTAGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTgcg                                                                                                             >  2:641914/1‑139 (MQ=255)

             aCCATATTTAGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTgcg                                                                                                             <  1:641914/139‑1 (MQ=255)

                      aGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGAcagca                                                                                                    >  1:345943/1‑139 (MQ=255)

                         gATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGAt                                                                                                 <  2:673031/139‑1 (MQ=255)

                         gATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGAt                                                                                                 >  1:356275/1‑139 (MQ=255)

                           tGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTg                                                                                               >  1:503970/1‑139 (MQ=255)

                             cGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGcc                                                                                                                                       <  1:255152/97‑1 (MQ=255)

                             cGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGcc                                                                                                                                       >  2:255152/1‑97 (MQ=255)

                             cGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGcc                                                                                             >  1:664168/1‑139 (MQ=255)

                                     gTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCTGCGACAGCAGATTGCCGACAATCa                                                                                     >  2:390531/1‑139 (MQ=255)

                                             cGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCgag                                                                             <  2:503970/139‑1 (MQ=255)

                                                tAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAgg                                                                          >  1:412185/1‑139 (MQ=255)

                                                     tATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGAc                                                                     <  2:664168/139‑1 (MQ=255)

                                                      aTTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCg                                                                                            >  1:541985/1‑115 (MQ=255)

                                                      aTTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCg                                                                                            <  2:541985/115‑1 (MQ=255)

                                                        tGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATc                                                                                      <  1:334263/119‑1 (MQ=255)

                                                        tGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATc                                                                                      >  2:334263/1‑119 (MQ=255)

                                                            aaaCAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGa                                                              <  2:345943/139‑1 (MQ=255)

                                                                  cGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGt                                                        >  1:504946/1‑139 (MQ=255)

                                                                  cGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGt                                                        >  1:670218/1‑139 (MQ=255)

                                                                    tAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGaa                                                             >  1:133510/1‑132 (MQ=255)

                                                                    tAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGaa                                                             <  2:133510/132‑1 (MQ=255)

                                                                     aaaGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACg                                                     <  2:356275/139‑1 (MQ=255)

                                                                         cGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCAc                                                 <  2:670218/139‑1 (MQ=255)

                                                                                      ggAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCg                                                                               >  2:561686/1‑96 (MQ=255)

                                                                                      ggAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCg                                                                               <  1:561686/96‑1 (MQ=255)

                                                                                      ggAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACcg                                    >  1:627161/1‑139 (MQ=255)

                                                                                            tCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGAcag                                                                                                      <  2:545891/67‑1 (MQ=255)

                                                                                            tCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGAcag                                                                                                      >  1:545891/1‑67 (MQ=255)

                                                                                                               aTACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACCGCGGTTCGGTCGGATCTTTAACaaaa           >  1:118139/1‑139 (MQ=255)

                                                                                                                        ggTGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACCGCGGTTCGGTCGGATCTTTAACAAAACGCGCCACg  >  1:150714/1‑139 (MQ=255)

CACCATCAGGATCACCATATTTAGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGTGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACCGCGGTTCGGTCGGATCTTTAACAAAACGCGCCACG  >  NC_000913/4567452‑4567710

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