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
A13 F1 I1 R1	778	68.7	3228504	93.4%	3015422	109.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,338,234	A→G	L396P (CTG→CCG)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,338,234	0	A	G	94.1%	106.1 / ‑2.1	34	L396P (CTG→CCG)	gyrA	DNA gyrase (type II topoisomerase), subunit A
Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (12/20); total (13/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.37e-01

AGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCAGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGAAAATAGTACGACGGGTCACCACTTCACGGCGGTGAC  >  NC_000913/2338111‑2338354

aGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGt                                                                                                           <  1:17320/139‑1 (MQ=255)

aGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGt                                                                                                           <  1:414913/139‑1 (MQ=255)

              cgcAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGGAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGAGCGGGTCGATGTTCGCCAgc                                                                                             >  1:1053513/1‑139 (MQ=255)

                cagcaTCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGt                                                                                                           <  2:274017/123‑1 (MQ=255)

                cagcaTCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGt                                                                                                           >  1:274017/1‑123 (MQ=255)

                       gtcgCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCt                                                                                    <  2:108662/139‑1 (MQ=255)

                                     cGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCAc                                                                                        >  2:488004/1‑121 (MQ=255)

                                     cGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCAc                                                                                        <  1:488004/121‑1 (MQ=255)

                                          aTCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGGCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAg                                                                 <  2:1053513/139‑1 (MQ=255)

                                              cgGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCAc                                                                                        <  1:1158253/112‑1 (MQ=255)

                                              cgGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCAc                                                                                        >  2:1158253/1‑112 (MQ=255)

                                                   aCGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATcgc                                                        <  2:976338/139‑1 (MQ=255)

                                                   aCGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGATCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATcgc                                                        <  2:590581/139‑1 (MQ=255)

                                                              cTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGc                                             <  2:362649/139‑1 (MQ=255)

                                                                 ccACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGt                                          >  1:187166/1‑139 (MQ=255)

                                                                      gATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGc                                                                                     <  2:776596/91‑1 (MQ=255)

                                                                      gATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGc                                                                                     >  1:776596/1‑91 (MQ=255)

                                                                      gATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGaa                                     <  2:490702/139‑1 (MQ=255)

                                                                               ccAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCaa                                                                          >  1:509340/1‑93 (MQ=255)

                                                                               ccAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCaa                                                                          <  2:509340/93‑1 (MQ=255)

                                                                                 aGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGc                                             <  2:387278/120‑1 (MQ=255)

                                                                                 aGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGc                                             >  1:387278/1‑120 (MQ=255)

                                                                                 aGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGAAAATAGTacgac                          >  1:1449853/1‑139 (MQ=255)

                                                                                  gcgcAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGAAAATAGTacgacg                         <  2:1449853/139‑1 (MQ=255)

                                                                                   cgcgGTTTTCGCTTCTGCAGGCGTCGGCTCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGAAAATAGTACGACgg                        <  2:672612/139‑1 (MQ=255)

                                                                                             gCTTCTGCAGGCGTCGGCGCATGACGGATCAGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTc                                        >  1:118358/1‑113 (MQ=255)

                                                                                             gCTTCTGCAGGCGTCGGCGCATGACGGATCAGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTc                                        <  2:118358/113‑1 (MQ=255)

                                                                                                  tGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTGCGCAGTTCGAAAATAGTACGACGGGTCACCACTTCAcgg         <  2:523589/139‑1 (MQ=255)

                                                                                                  tGCAGGCGTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGAAAATAGTACGACGGGTCACCACTTCAcgg         <  1:765686/139‑1 (MQ=255)

                                                                                                         gTCGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGAAAATAGTACGACGGGTCACCACTTCACGGCGGTGAc  >  2:261997/1‑139 (MQ=255)

                                                                                                           cGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATcgc                                                        >  2:145621/1‑83 (MQ=255)

                                                                                                           cGGCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATcgc                                                        <  1:145621/83‑1 (MQ=255)

                                                                                                            ggCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTaa                                                                                  <  2:3400/56‑1 (MQ=255)

                                                                                                            ggCGCATGACGGATCGGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTaa                                                                                  >  1:3400/1‑56 (MQ=255)

AGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATGACGGATCAGTTCGATGATCGGGTCGATGTTCGCCAGCGCCACGGCTAATGCTTCAAGGATATGAGCACGATCGCGAGCTTTACGCAGTTCGAAAATAGTACGACGGGTCACCACTTCACGGCGGTGAC  >  NC_000913/2338111‑2338354

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