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
A14 F56 I20 R2 1958 92.1 3575798 91.1% 3257551 126.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP006881 2,197,594 G→A L182L (CTG→TTG)  U712_11010 ← Chorismate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068812,197,5940GA98.1% 159.6 / NA 53L182L (CTG→TTG) U712_11010Chorismate synthase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (30/22);  minor base T (0/1);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 4.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACAATGACTTCTACAATTCCGCCGATGGAATCTCCGTTGGCCTTCGCTTCATCAATGGCAGCCATCATTTTTTTGCCCGCTTCTTCATCGTAGCATCTGACCGGAGACTCCTCCGTTACACGCTGCAGGTCATCAATTGACGTATATTCTGTTTTTTCAGCTTTAACTGCGCCAATTTGCAATACGTGACCTGCCACCTTAATGCCGAGCTCAGAAAGAATCTTTTTAGCGACAGCTCCTGCCGCCACTCTGACAGTTGTTT  >  CP006881/2197466‑2197728
                                                                                                                                |                                                                                                                                      
gACAATGTCTTCTACTATTCCGCCGATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCaa                                                                                                                                <  3:378828/137‑1 (MQ=255)
gACAATGACTTCTACTATTCCGCCGATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCaa                                                                                                                                <  2:17903/137‑1 (MQ=255)
gACAATGACTTCTACTATTCCGCCGATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCaa                                                                                                                                <  7:21415/137‑1 (MQ=255)
gACAATGACTTCTACTATTCCGCCGATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAAtt                                                                                                                              <  1:79348/139‑1 (MQ=255)
   aaTGACTTCTACTATTCCGCCGATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGAc                                                                                                                           <  4:234252/139‑1 (MQ=255)
   aaTGACTTCTACTATTCCGCCGATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGAc                                                                                                                           <  2:200164/139‑1 (MQ=255)
     tGACTTCTACTATTCCGCCGATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAAATGACg                                                                                                                          >  4:142479/1‑138 (MQ=255)
                 ttCCGCCGATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCCTCGTAGCATCTGACAGGAGACTCTTCCGTTACCCGCTGCAAGTCTTCAATTGACGTATACTCTGtttt                                                                                                             >  3:81987/1‑139 (MQ=255)
                 ttCCGCCGATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGtttt                                                                                                             >  8:56492/1‑139 (MQ=255)
                 ttCCGCCGATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGtttt                                                                                                             >  7:99477/1‑139 (MQ=255)
                   ccgccgATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGttttt                                                                                                            <  2:345883/138‑1 (MQ=255)
                   ccgccgATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGttttt                                                                                                            >  3:54023/1‑138 (MQ=255)
                   ccgccgATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGttttt                                                                                                            <  2:357099/138‑1 (MQ=255)
                   ccgccgATGGAATCTACGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGttttt                                                                                                            <  2:383465/138‑1 (MQ=255)
                    cgccgATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTc                                                                                                          <  8:99477/139‑1 (MQ=255)
                      ccgATGGAATCTCCGTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAg                                                                                                        >  5:357860/1‑139 (MQ=255)
                                    gTTTGCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCa                                                                                          <  4:54023/139‑1 (MQ=255)
                                       tgCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTc                                                                                                                   >  7:229398/2‑111 (MQ=255)
                                       tgCCTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTc                                                                                                                   <  8:229398/110‑1 (MQ=255)
                                          cTTTGCTTCATCAATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGc                                                                                    <  3:169575/139‑1 (MQ=255)
                                                   atcaATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTc                                                                                                          >  6:174221/1‑108 (MQ=255)
                                                   atcaATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTc                                                                                                          <  5:174221/108‑1 (MQ=255)
                                                   atcaATGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTgg                                                                           >  7:3946/1‑138 (MQ=255)
                                                        tttcatccATCTTTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATATGCAACACGTGGCCCGc                                                                      <  1:424370/133‑1 (MQ=255)
                                                        tGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGc                                                                      <  6:357860/139‑1 (MQ=255)
                                                        tGGCAGCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGc                                                                      <  5:251040/139‑1 (MQ=255)
                                                             gCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCt                                                                 <  1:194088/139‑1 (MQ=255)
                                                             gCCATCATTTTTTTGCCTGCCTCTTCATCGTAGCATCTGACAGGAGACTCTTCCGGTAAACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCACGCCACCt                                                                 >  6:212272/1‑139 (MQ=255)
                                                                                 ctcttcATCGAAGCTTCTGACAGGTGACTCTTCCGTTACACGCTGCATGGCTTCAATTGCCTTATACTCTGTTTTTTCAGCTTTAACAGCACCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCagaaaga                                             <  4:202173/138‑1 (MQ=255)
                                                                                           tAGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAg                                   >  4:364041/1‑139 (MQ=255)
                                                                                            aGCATCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGc                                  >  7:429960/1‑139 (MQ=255)
                                                                                            aGCATATGACAGGATACTCTTCATTAACAAGCAGCAAGTCTTCAAATGACGTATACTCTCTATTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCACGCCACCTTAATGCCAAGCTCAGAAAGAATCtttt                                      >  6:90409/1‑135 (MQ=255)
                                                                                                tCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGcta                                >  5:279050/1‑135 (MQ=255)
                                                                                                tCTGACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGcta                                >  3:56044/1‑135 (MQ=255)
                                                                                                   gACAGGAGACTCTTCCGTTACCCGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCAAATTTGCAACACGTGGCCAGCCACCTTAATGACAAGCTAAGAAAGAATCTTTTTAGCTACatcc                           >  8:22065/1‑136 (MQ=255)
                                                                                                   gACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGcc                           >  8:74225/1‑138 (MQ=255)
                                                                                                   gACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGcc                           >  5:439260/1‑138 (MQ=255)
                                                                                                   gACAGGAGACTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGcc                           >  8:15602/1‑138 (MQ=255)
                                                                                                     caggAGACTCTTCCGTTACACGCTGCAAGTCTTCAAATGACGTATACTCTGTATATTCAGCAATAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGcccc                         <  3:142479/137‑1 (MQ=255)
                                                                                                        gagaCTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCGTAATGCCAAGCTCAGAAAGAATCTTGTTAGCTACAGCCCCTgc                      >  8:169235/1‑139 (MQ=255)
                                                                                                           aCTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTgccgc                   >  7:180844/1‑139 (MQ=255)
                                                                                                           aCTCTTCCGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGAAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTgccgc                   >  4:134128/1‑139 (MQ=255)
                                                                                                               ttccGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCAct               >  1:181724/2‑139 (MQ=255)
                                                                                                                 ccGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCAc                <  3:364041/136‑1 (MQ=255)
                                                                                                                  cGTTACACGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCActct             <  7:74225/138‑1 (MQ=255)
                                                                                                                         cGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGc                                                                      >  2:439951/1‑74 (MQ=255)
                                                                                                                         cGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGc                                                                      <  1:439951/74‑1 (MQ=255)
                                                                                                                         cGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAgttg     >  3:184275/1‑139 (MQ=255)
                                                                                                                         cGCTGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAgttg     >  6:218238/1‑139 (MQ=255)
                                                                                                                            tGCAAGTCTTCAATTGACGTTTACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCACGCCACCTTAAGGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCAACGCTGCCAgttgtt   >  8:278346/1‑138 (MQ=255)
                                                                                                                            tGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCCCTCTGACAGTTGttt  >  4:144643/1‑139 (MQ=255)
                                                                                                                            tGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGttt  >  2:49567/1‑139 (MQ=255)
                                                                                                                            tGCAAGTCTTCAATTGACGTATACTCTGTTTTTTCAGCTTTAACAGCGCCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGttt  >  2:28854/1‑139 (MQ=255)
                                                                                                                                |                                                                                                                                      
GACAATGACTTCTACAATTCCGCCGATGGAATCTCCGTTGGCCTTCGCTTCATCAATGGCAGCCATCATTTTTTTGCCCGCTTCTTCATCGTAGCATCTGACCGGAGACTCCTCCGTTACACGCTGCAGGTCATCAATTGACGTATATTCTGTTTTTTCAGCTTTAACTGCGCCAATTTGCAATACGTGACCTGCCACCTTAATGCCGAGCTCAGAAAGAATCTTTTTAGCGACAGCTCCTGCCGCCACTCTGACAGTTGTTT  >  CP006881/2197466‑2197728

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A