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
A8 F1 I1 R1	771	44.8	2153074	94.1%	2026042	109.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,190,144	G→A	P102S (CCG→TCG)	phoP ←	response regulator in two‑component regulatory system with PhoQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,190,144	0	G	A	90.0%	150.9 / 8.8	61	P102S (CCG→TCG)	phoP	response regulator in two‑component regulatory system with PhoQ
Reads supporting (aligned to +/- strand): ref base G (3/3); new base A (29/25); total (32/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.43e-01

GTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCT  >  NC_000913/1190013‑1190278

gTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTc                                                                                                                                 <  2:277817/139‑1 (MQ=255)

  cATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTGTTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTcac                                                                                                                               >  1:628495/1‑139 (MQ=255)

      aaTAGACAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATaa                                                                                                                           >  1:735881/1‑139 (MQ=255)

       aTAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACGGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAat                                                                                                                          >  2:224720/1‑139 (MQ=255)

           aTAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAatcatc                                                                                                                      >  1:828505/1‑139 (MQ=255)

               ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCa                                                                                                                  >  1:193028/1‑139 (MQ=255)

               ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCa                                                                                                                  >  2:492387/1‑139 (MQ=255)

                  aCGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCg                                                                                                               >  2:1072969/1‑139 (MQ=255)

                    ggCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGc                                                                                                             >  1:630517/1‑139 (MQ=255)

                    ggCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGc                                                                                                             >  2:475310/1‑139 (MQ=255)

                     gCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTGTTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCa                                                                                                            <  2:628495/139‑1 (MQ=255)

                        agagagaTCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTa                                                                                                                                    <  2:841675/112‑1 (MQ=255)

                        agagagaTCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTa                                                                                                                                    >  1:841675/1‑112 (MQ=255)

                          agagaTCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAg                                                                                                                                   >  2:315654/1‑111 (MQ=255)

                          agagaTCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAg                                                                                                                                   <  1:315654/111‑1 (MQ=255)

                                        aaCGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGt                                                                                         >  2:816949/1‑139 (MQ=255)

                                             ggggAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGc                                                                                    >  1:954614/1‑139 (MQ=255)

                                              gggAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGcc                                                                                   >  1:123007/1‑139 (MQ=255)

                                                   cGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCg                                                                                                               >  2:824058/1‑106 (MQ=255)

                                                   cGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCg                                                                                                               <  1:824058/106‑1 (MQ=255)

                                                      aaTGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCa                                                                           <  1:475310/139‑1 (MQ=255)

                                                          aCCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  2:954614/139‑1 (MQ=255)

                                                          aCCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  1:1072969/139‑1 (MQ=255)

                                                             tgtgAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCgg                                                                    >  1:1025651/1‑139 (MQ=255)

                                                              ttgAAGCCATACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCACCACCTCTTCAATATGAAACGCTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGggtggt                                                                   <  2:193028/138‑1 (MQ=255)

                                                                    ccAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTcc                                                                                       >  2:40479/1‑113 (MQ=255)

                                                                    ccAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTcc                                                                                       <  1:40479/113‑1 (MQ=255)

                                                                     cAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATAcc                                                            <  2:14973/139‑1 (MQ=255)

                                                                      aGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCa                                                           >  2:39468/1‑139 (MQ=255)

                                                                        aCCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTa                                                                                                                                    <  2:925269/64‑1 (MQ=255)

                                                                        aCCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTa                                                                                                                                    >  1:925269/1‑64 (MQ=255)

                                                                         ccGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       >  2:335204/1‑124 (MQ=255)

                                                                         ccGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  1:335204/124‑1 (MQ=255)

                                                                           gCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATc                                                      <  1:39468/139‑1 (MQ=255)

                                                                             tATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAg                                                                                                                                   >  1:192149/1‑60 (MQ=255)

                                                                             tATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAg                                                                                                                                   <  2:192149/60‑1 (MQ=255)

                                                                                  cgccgcATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTg                                               <  2:1025651/139‑1 (MQ=255)

                                                                                       cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCa                                                                                  >  2:76072/1‑99 (MQ=255)

                                                                                       cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCa                                                                                  <  1:76072/99‑1 (MQ=255)

                                                                                       cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACgg                                                                        >  1:951507/1‑109 (MQ=255)

                                                                                       cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACgg                                                                        <  2:951507/109‑1 (MQ=255)

                                                                                       cATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACa                                          >  1:731306/1‑139 (MQ=255)

                                                                                        aTTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACAt                                         <  1:224720/139‑1 (MQ=255)

                                                                                         ttAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATc                                        <  2:792272/139‑1 (MQ=255)

                                                                                             tGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTg                                    >  2:900260/1‑139 (MQ=255)

                                                                                                    aTTCGCGCCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGcc                             <  1:492387/139‑1 (MQ=255)

                                                                                                         cgcCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATc                                                      >  1:206123/1‑109 (MQ=255)

                                                                                                         cgcCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATc                                                      <  2:206123/109‑1 (MQ=255)

                                                                                                          gcCATCACCTCTTCAATATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAgcggc                       <  1:900260/139‑1 (MQ=255)

                                                                                                                    ctTCAATATGAAACGATTTAGTCACATAATCATCAGCACCg                                                                                                               >  2:616851/1‑41 (MQ=255)

                                                                                                                    ctTCAATATGAAACGATTTAGTCACATAATCATCAGCACCg                                                                                                               <  1:616851/41‑1 (MQ=255)

                                                                                                                        aaTATGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGAAAGa         <  2:630517/139‑1 (MQ=255)

                                                                                                                            tGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       <  1:229600/73‑1 (MQ=255)

                                                                                                                            tGAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACggg                                                                       >  2:229600/1‑73 (MQ=255)

                                                                                                                             gAAACGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTc    <  2:735881/139‑1 (MQ=255)

                                                                                                                               aaCGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCt  >  2:712674/1‑139 (MQ=255)

                                                                                                                               aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACtt                                                                                                  <  1:190807/43‑1 (MQ=255)

                                                                                                                               aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACtt                                                                                                  >  2:190807/1‑43 (MQ=255)

                                                                                                                               aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCg                                                                                                >  2:694491/1‑45 (MQ=255)

                                                                                                                               aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCg                                                                                                <  1:694491/45‑1 (MQ=255)

                                                                                                                               aaCGATTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCt  >  2:952087/1‑139 (MQ=255)

GTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTTCGACTTTGTCCTGCCAGCTTTCACGGGCGGTTAATACCAGAATCGGCAGTGAAACATCGTTGCTACGCCAGCGGCGAATCAGTGACAGACCGTCCT  >  NC_000913/1190013‑1190278

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `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