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 I2 R1	67	27.9	1239648	95.3%	1181384	112.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,384,861	G→A	Q341Q (CAG→CAA)	yjeM →	putative transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,384,861	0	G	A	75.0%	50.6 / 17.0	32	Q341Q (CAG→CAA)	yjeM	putative transporter
Reads supporting (aligned to +/- strand): ref base G (4/4); new base A (12/12); total (16/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCACTGCATTTGTCACCTGAAGCGTCATTGTCGCTGGGCGTATGGTTTGCGCGTATTACTGGACTTTCGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAGGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGGGTTGGTTACTGTCTTCATCCTGCTGGTTTCGTTTGGTGGCGGTACCG  >  NC_000913/4384727‑4384994

gCACTGCATTTGTCACCTGAAGCGTCATTGTCGCTGGGCGTATGGTTTGCGCGTATTACTGGACTTACGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGa                                                                                                                                   >  2:377199/1‑139 (MQ=255)

                  gAAGCGTCATTGTCGCTGGGCGTATGGTTTGCGCGTATTACTGGACTTTCGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAGGGGACGCCGAAAGCATTGTGGc                                                                                                                 <  2:373098/139‑1 (MQ=255)

                   aaGCGTCATTGTCGCTGGGCGTATGGTTTGCGCGTATTACTGGACTTTCGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGcc                                                                                                                >  1:447962/1‑139 (MQ=255)

                              tCGCTGGGCGTATGGTTTGCGCGTATTACTGGACTTTCGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAGGGGACGCCGAAAGCATTGTGGCCGGAACCGATGa                                                                                                     >  2:372096/1‑139 (MQ=255)

                                gCTGGGCGTATGGTTTGCGCGTATTACTGGACTTTCGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGAcg                                                                                                   <  2:121766/139‑1 (MQ=255)

                                       gTATGGTTTGCGCGTATTACTGGACTTTCGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGa                                                                                            <  1:161187/139‑1 (MQ=255)

                                                            ggACTTTCGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTa                                                                       <  1:303253/139‑1 (MQ=255)

                                                                  tCGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAGGGGACGCCGa                                                                                                                             >  2:579037/1‑79 (MQ=255)

                                                                  tCGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAGGGGACGCCGa                                                                                                                             <  1:579037/79‑1 (MQ=255)

                                                                                  ataCCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACGGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGccg                                                 >  1:364700/1‑137 (MQ=255)

                                                                                        gTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCa                                                                                                                        >  1:166330/1‑62 (MQ=255)

                                                                                        gTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCa                                                                                                                        <  2:166330/62‑1 (MQ=255)

                                                                                          gCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGcc                                                                            <  1:465332/104‑1 (MQ=255)

                                                                                          gCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGcc                                                                            >  2:465332/1‑104 (MQ=255)

                                                                                           cGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGGGTTGGTTAc                                        <  1:69060/139‑1 (MQ=255)

                                                                                                    cGCTTTGCTATTCACCGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGGGTTGGTTACTGTCTTCAt                               <  1:369465/139‑1 (MQ=255)

                                                                                                     gCTTTGCTATTCACCGTTGAAAGCCATCATCCAGGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGGGTTGGTTACTGTCTTCATc                              >  1:218184/1‑139 (MQ=255)

                                                                                                                   cGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTAt                                                                      <  1:265963/85‑1 (MQ=255)

                                                                                                                   cGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTAt                                                                      >  2:265963/1‑85 (MQ=255)

                                                                                                                   cGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGc                                                                   <  2:415955/88‑1 (MQ=255)

                                                                                                                   cGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGc                                                                   >  1:415955/1‑88 (MQ=255)

                                                                                                                   cGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGt                                                     >  2:93287/1‑102 (MQ=255)

                                                                                                                   cGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGt                                                     <  1:93287/102‑1 (MQ=255)

                                                                                                                   cGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGGGTTGGTTACTGTCTTCATCCTGCTGGTTTCGtt                >  1:521058/1‑139 (MQ=255)

                                                                                                                   cGTTGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGGGTTGGTTACTGTCTTCATCCTGCTGGTTTCGtt                >  2:73727/1‑139 (MQ=255)

                                                                                                                     ttGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGa                                                           <  2:280497/94‑1 (MQ=255)

                                                                                                                     ttGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGa                                                           >  1:280497/1‑94 (MQ=255)

                                                                                                                     ttGAAAGCCATCATCCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGGGTTGGTTACTGTCTTCATCCTGCTGGTTTCGTTtg              >  2:196899/1‑139 (MQ=255)

                                                                                                                              atcatcCAAGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGGGTTGGTTACTGTCTTCATCCTGCTGGTTTCGTTTGGTGGCGGTa     <  1:182114/139‑1 (MQ=255)

                                                                                                                                 atcCAGGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGGGTTGGTTACTGTCTTCATCCTGCTGGTTTCGTTTGGTGGCGGTACCg  <  2:218184/139‑1 (MQ=255)

                                                                                                                                     aGGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGggt                                               <  1:507325/90‑1 (MQ=255)

                                                                                                                                     aGGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGggt                                               >  2:507325/1‑90 (MQ=255)

GCACTGCATTTGTCACCTGAAGCGTCATTGTCGCTGGGCGTATGGTTTGCGCGTATTACTGGACTTTCGATGTTCCTCGCCTATACCGGTGCGTTCTTTACGCTTTGCTATTCACCGTTGAAAGCCATCATCCAGGGGACGCCGAAAGCATTGTGGCCGGAACCGATGACGCGCCTGAATGCGATGGGGATGCCGTCTATCGCCATGTGGATGCAGTGCGGGTTGGTTACTGTCTTCATCCTGCTGGTTTCGTTTGGTGGCGGTACCG  >  NC_000913/4384727‑4384994

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